Here are a few things to consider :

Tactics

If a full attack is "all" it takes to down someone, force Move actions. Could come from cover/concealment or combat maneuvers like Trip/Knockdown or Disarm. If you just play "rocket tag", you're implicitly accepting that if you miss, there's a good chance you're dead.

Note that this is exactly what happens IRL between powerful forces in a battle and in this respect, is not a "bug" of the system but a simple truth.

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Intelligence

So you're targeted by a Master Ninja, who manages to sneak up on you and place a Death attack. Curse you, Hayabusa ! Wait, you made your save ! Time to grab your trusty bow and fill him with arrows...
Well, boo. The ninja has broken/stolen your bow as well. Not only does he make his escape, he's slowed you down by forcing you to have it repaired / replaced while you try to get it back.

This goes a step further in Tactics, and is to be expected of Ninja, for example. Study your target. Know their strengths and weaknesses as well as yours. "That Brilliant Bow of Badassitude could be a problem if I must escape. Can I get rid of it ? What about impairing the bowman ? Maybe I could blind him ?"

As an aside, the GM should make sure the players don't feel cheated though. Extreme competence is assumed as part of the characters (especially past level 10) and robbing them of that can be frustrating to no end for some.

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Numbers

So they can take the Big-Ass-Monster down in a round ? What about 10 Medium-Sized-Nuisances ? One by itself could barely hope to hit them, but with flanking, teamwork feats and simply being all over the place, the little pests could prove to be annoying. Add in a Leader-type and you could even be worrying your characters.

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Story happens

Take the characters down a notch or two through Story. Have them stripped of Rank and Privileges by the King or even make them straight Outlaws. Have them stranded on an island (and some of their equipment lost to the sea) after their boat got caught in a storm. Have their home base attacked (and their Mentor killed, leaving them unable to progress in their main class) while they were on mission.

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Change focus for a while

Once all is said and done, if the combat has become so easy it's boring, it may be time to try a little courtly intrigue for a change. Or why not a mystery ? Possibly meshing with "Story happens" above, there are plenty of opportunities to take the players / characters out of their comfort zone while staying true to the setting. They'll be happy to resume bashing heads once they've stumbled for hours finding a tangible threat to pounce on. Or hey, maybe they'll actually enjoy trading piques with the Jester and decide they want a piece of land and a throne of their own ?

Homebrew

This is not official material; I’m making it up. For what it’s worth, I’m fairly good at it (won several 3.5 homebrew competitions; did freelance work for Legend and Pathfinder, each a 3.5-spinoff; wrote a “book” about it as a question answer), but don’t mistake this for official material. You’ll have to ask your DM about it. I would love to hear feedback on it, whether or not you use it. If you do, I’d really love to know how it plays.

Ultimately, this variant of the druid has one major advantage and one major disadvantage, with respect to the regular druid. The advantage is that the swarms the swarm druid calls are inherently expendable; you can call up a new quite quickly relative to training a new animal companion. This means you can scout dangerous areas more easily. The disadvantage is in the swarms themselves: you have far fewer options for calling a swarm or adopting a swarm shape than a druid does for bonding an animal companion or assuming a wild shape.

Swarm Druid variant

The swarm druid is a variant class option for the druid; except as noted here, the class is identical to the druid in every way. You cannot multiclass between swarm druid and regular druid, or any other druid variant, but you may take advantage of alternative class features that replace those class features that the swarm druid does have.

Spells

As a regular druid, except with the addition of the following spells:

1. Buzzing bee,^SC cause fear, deathwatch, ebon eyes,^SC nerveskitter,^SC spirit worm^SC
2. Darkness, death knell, scare, web
3. Chain of eyes,^SC deeper darkness, gaseous form, spider poison,^SC stinking cloud, tremorsense^SC
4. Fear
5. Cloudkill, crawling darkness,^SC plague of rats,^SC prying eyes
6. Fire spiders,^SC spider plague^SC
7. Brain spider^SC
8. Greater prying eyes
9. Otyugh swarm^SC

Spells marked ^SC are from Spell Compendium.

Bonus Languages

As a swarm druid, you still learn druidic as a free language and are still barred from teaching it to non-druids.

However, instead of adding Sylvan as a bonus language, you add Undercommon, the language of dark places, and perhaps more importantly, the drow. Even if you are not a drow, the drow’s long history of working with vermin and swarms means it is important for many swarm druids to be able to interact with them. If you do learn Undercommon (whether as a bonus language or not), you count as a drow for the sake of meeting the prerequisites of feats or prestige classes that have to do with vermin or swarms, and drow treat you as they would other drow (which is not that well, but as far as it goes).

Call Swarm (Ex)

You may call together a swarm almost anywhere; even desolate deserts usually have spiders and scorpions hidden under the sands. The swarm’s members are called from the immediate surroundings. In the rare cases where there are not sufficient options in the immediate area, you may draw them from great distances, though this makes the call take longer.

Calling the swarm is a full-round action. Provided the environment you are in would be able to provide sufficient creatures for the swarm in a square mile centered on you, the swarm is fully gathered by the end of your calling, as eligible creatures tend to be drawn to you before you even call.

If this area would not have sufficient creatures, consider an area with a 1½ mile radius; if this would be sufficient, the swarm has gathered by the start of your next turn. For every additional mile in the radius before enough creatures may be found, it takes another round for the swarm to form, always becoming available at the start of your turn. You do not need to continue calling while the swarm is forming.

The called swarm remains together and with you for as long as you wish it to. You do not need to concentrate on its continued existence. It disperses either when you tell it to or when the swarm creature dies. You may order a swarm to disperse but follow you, out of sight, so that you may call it again without worrying about whether there are enough creatures in the area. The DM may determine that there are some places the swarm cannot go or barriers it cannot cross, or at least cannot go without coming out of the woodwork and reforming as a swarm. If this happens, you are aware of it. If you leave a swarm or tell it to go away, the individual creatures will gradually return from where they came. You cannot tell a group of swarm-capable creatures to remain in an area as you leave, unless you leave it as a cohesive swarm.

You may only have one swarm at a time. A swarm you have disbanded but continue to have with you counts as this swarm. Calling a new swarm causes the previous one to gradually disperse and return from where it came.

See Swarm Druid’s Called Swarm, below, for more details on the swarm itself.

Beginning at 8th level, you may call swarms from any distance, even from other planes. This is a supernatural action that takes 1 round to complete; at the end of the action, your called swarm is ready, no matter where you are. This is a Conjuration (Calling) effect.

This feature replaces the druid’s regular animal companion class feature. Any feature that augments or improves your animal companion may improve your called swarm. Any other class that grants an animal companion that stacks with druid levels may instead stack with your swarm druid levels for your called swarm. If you choose to forgo this option and gain an animal companion instead, swarm druid levels do not count towards it, and you cannot change this choice for that class once made.

Eusociality (Ex)

You can improve the attitude of any swarm. This functions just like a Diplomacy check made to improve the attitude of a person. You roll 1d20 and add your class level and your Charisma modifier to determine the check result.

A swarm of creatures used to life within humanoid civilization (“indoor” species of ants, cockroaches, spiders, and so on) usually have a starting attitude of indifferent, while species in the wilderness usually start as unfriendly.

To make this check, you and the swarm must be able to study each other, which for many swarms requires sharing the swarm’s space. In such cases, you roll your check upon entering the swarm (or the swarm covering you), and if it is successful, the swarm will not attack you.

You may also make this check to improve the attitude of vermin without the swarm subtype, but do so at a −4 penalty.

Additionally, you are immune to the Distraction special attack of any creature with the swarm subtype. This is true even of swarms that you do not improve the attitude of.

This class feature replaces wild empathy. Any feature that augments or improves wild empathy may improve eusociality. Any other class that grants wild empathy that stacks with druid levels may instead stack with your swarm druid levels for eusociality. If you choose to forgo this option and gain wild empathy instead, swarm druid levels do not count towards it, and you cannot change this choice for that class once made.

This class feature counts as the Verminfriend feat (Drow of the Underdark) for the purposes of prerequisites. You may still take that feat if you meet its requirements.

Swarm Trainer (Ex)

You may train mindless swarms, as well as swarms with Intelligence scores of 1 or 2, by using the Handle Animal skill, even if the swarm is not composed of animals. More intelligent swarms must be interacted with using the usual social skills, or eusociality, not Handle Animal.

Mindless swarms are considered to have Intelligence 1 for the purposes of training them and their ability, once trained, to execute tricks and other commands. They are still considered mindless for all other purposes, including affecting them with mind-affecting magic.

This class feature replaces nature sense. It also counts as the Vermin Trainer feat (Drow of the Underdark) for prerequisites. You may still take Vermin Trainer as a feat if you meet its requirements.

Hivemind (Su)

Beginning at 2nd level, any swarm you share a space with reports information back to you. Generally speaking, the information is what the swarm collectively sees, smells, hears, and feels. This is not the same as actually experiencing those sensations yourself (but see the Sensory Feedback feature that swarms called by high-level swarm druids get), but it is sufficient to pin-point creatures you cannot sense yourself that share a space with the same swarm you do.

Resist the Swarm (Ex)

At 4th level, you gain a +4 bonus on all saving throws made against the special attacks and special qualities of swarms.

This feature replaces the resist nature’s lore class feature that a regular druid receives.

Swarm Shape (Su)

At 5th level, you gain the ability to turn yourself into a swarm once per day. This feature otherwise functions exactly as does a regular druid’s wild shape, which it replaces, except that instead of turning into an animal, you turn into an animal or vermin with the swarm subtype.

Swarm shape may be used in place of wild shape for prerequisites, and daily uses of swarm shape count as daily uses of wild shape and may be expended in much the same way for wild feats and the like. Feats and features that modify wild shape may modify swarm shape.

Class levels that stack with druid levels for wild shape instead stack with swarm druid levels for swarm shape. If a class grants wild shape to those that don’t have it, you may either gain wild shape and the levels don’t stack, or else choose to stack those levels with swarm druid levels for swarm shape. This choice, once made, cannot be changed for that class.

Like the regular druid, you more daily uses of this ability at 6th, 7th, 10th, 14th, and 18th level, as noted in Table: The Druid.

At 8th, 11th, and 15th level, you gain the ability to shape yourself into two, three, and four swarms at the same time. All swarms must be adjacent to each other and either include or be adjacent to the space you occupied before assuming the shape. When you shape into multiple swarms, divide your HP evenly among them; when you return to your own shape, add the remaining HP totals to determine your remaining HP. You die only if all swarms you are shaped in die. This replaces the druid’s ability to turn into larger and smaller creatures.

At 12th level, you add the fey, plant, and ooze types to the list of creature types you can turn into with swarm shape. The chosen creature must still have the swarm subtype and meet all criteria for wild shape aside from type and subtype. This replaces the druid’s ability to wild shape into plant forms.

At 16th level, you can use swarm shape to turn into swarms with the elemental type, once per day. This daily elemental swarm shape is in addition to your normal swarm shape usage. In addition to the normal effects of wild shape, you gain all the elemental swarm’s extraordinary, supernatural, and spell-like abilities. You also gain the elemental swarm’s feats for as long as you maintain the wild shape, but you retain your own creature type. This replaces the druid’s ability to wild shape into elemental forms.

At 18th and 20th levels, you can assume the form of an elemental swarm another time each day.

At 20th level, you can turn into a swarm of any type by using a use of the elemental swarm shape feature, gaining all special attacks and qualities as you would with elemental swarms. This replaces the druid’s ability to wild shape into huge elementals.

Swarm Druid’s Called Swarm

The swarm that you may call as a swarm druid is different from a normal swarm in many ways, as described below.

Training your called swarm

You may train the swarm you call using Handle Animal, as if it were an animal with Intelligence 2. As you gain more swarm druid levels, the swarm may also learn bonus tricks; see below. Each time you call a swarm, it comes trained in the same tricks as the previous swarm, though each trick must be taught in its entirety to a single swarm. Thus your called swarm can be trained, even though the swarm itself is composed of entirely different creatures each time you call it.

Called swarm bonuses

Use the base statistics for a creature of the called swarm’s kind, but make the following changes.

Class Level

Your swarm druid level. Your class level stacks with levels of any other classes that are entitled to an animal companion or to call a swarm for the purpose of determining the companion’s abilities and the alternative lists available to the character.

Bonus HD

Extra racial hit dice as appropriate to the swarm’s type. For most swarms, this means Animal or Vermin hit dice, which are both d8s that get +¾ BAB and 2+Int skill points per level. Animals get good Fortitude and Reflex saves, while Vermin only get good Fortitude saves.

DC Adj.

The number noted here is added to the saving throw DC of any special attacks or qualities, poisons, and so on that the called swarm has.

Space

The swarm’s space increases by the number noted here. As usual with swarms, this space is far more malleable than a typical creature’s.

Bonus Tricks

The value given in this column is the total number of “bonus” tricks that the swarm knows in addition to any that you might choose to teach it (see the Training the swarm, above). These bonus tricks don’t require any training time or Handle Animal checks, and they don’t count against the normal limit of tricks known by the swarm. The druid selects these bonus tricks each time he calls a swarm, but they cannot be changed for that swarm thereafter.

Link (Ex)

You can handle your called swarm as a free action, or push it as a move action, even if you don’t have any ranks in the Handle Animal skill. You gain a +4 circumstance bonus on all eusociality checks and Handle Animal checks made regarding a called swarm.

Share Spells (Ex)

At your option, you may have any spell (but not any spell-like ability) you cast upon yourself also affect your called swarm. You must be within the swarm’s space at the time of casting to receive the benefit.

Additionally, you may cast a spell with a target of “You” on your called swarm (as long as the swarm is covering you) instead of on yourself.

You and your called swarm can share spells even if the spells normally do not affect creatures of the swarm’s type.

Evasion (Ex)

If a called swarm is subjected to an attack that normally allows a Reflex saving throw for half damage, it takes no damage if it makes a successful saving throw.

Sensory Feedback (Su)

You are automatically aware of anything your called swarm can sense, at a distance of up to a mile. All checks made to use these senses, however, are made at the swarm’s bonus, not your own, which may make it difficult to understand what it is that the swarm is seeing or hearing. Touch, however, is often far more effective. When your called swarm is sharing a space with a creature or object, you know exactly where that creature is, how it is moving, its texture, and so on, even if the creature is invisible and silent. Incorporeal or ethereal creatures, however, are typically not felt.

Improved Evasion (Ex)

When subjected to an attack that normally allows a Reflex saving throw for half damage, a called swarm takes no damage if it makes a successful saving throw and only half damage if the saving throw fails.

Called Swarm Options

You cannot necessarily call together just any swarm, even if the creatures to make up the swarm are available.

Basic options

As a 1st-level swarm druid, you may call the following swarms together:

• Bat swarm
• Demonet swarm (Monster Manual IV)
• Leech swarm¹ (Stormwrack)
• Rat swarm
• Spider swarm
• Wasp swarm (Fiend Folio)
• Minor swarm²

Alternative Swarms

If you are a swarm druid of sufficiently high level, you may call swarms from one of the following lists, applying the indicated adjustment to your swarm druid level (in parentheses) for purposes of determining the swarm’s characteristics and abilities.

4th level or Higher (Level −3)

• Cranium rat swarm, lesser pack (Fiend Folio)
• Locust swarm
• Tomb spider broodswarm (Monster Manual IV)
• Viper swarm (Fiend Folio)

7th level or Higher (Level −6)

• Centipede swarm
• Bone rat swarm (Libris Mortis)
• Piranha swarm¹ (Stormwrack)
• Rylkspawn swarm (Monster Manual V)

10th level or Higher (Level −9)

• Broodswarm (Fiendish Codex I)
• Corpse rat swarm (Libris Mortis)
• Ephemeral swarm (Monster Manual III)
• Jellyfish swarm¹ (Stormwrack)
• Pest swarm (Cityscape)
• Plague ant swarm (Fiend Folio)
• Rapture locust swarm (Fiend Folio)
• Scorpion swarm (Sandstorm)
• Swamp strider swarm (Monster Manual III)

13th level or Higher (Level −12)

• Cranium rat swarm, average pack (Fiend Folio)
• Death scarab swarm (Sandstorm)
• Dread bloom swarm (Monster Manual III)
• Bloodmote cloud swarm (Libris Mortis)
• Mageripper swarm (Monster Manual IV)
• Needletooth swarm (Monster Manual III)

16th level or Higher (Level −15)

• Bloodfiend locust swarm (Fiend Folio)
• Cinder swarm (Monster Manual II)
• Hellwasp swarm
• Shimmering swarm (Monster Manual III)
• Brood keeper larva swarm (Monster Manual III)

¹ Can only be called into an aquatic environment.

² New monster presented below

Minor Swarm

• Size/Type: Dimuntive Vermin (swarm)
• Hit Dice: 2d8 (9 hp)
• Speed: 25 ft. (see text)
• Attack: Swarm (1d4)
• Space/Reach: 10 ft./0 ft.
• Special Attacks: Distraction
• Special Qualities: Immune to weapon damage, swarm traits, vermin traits
• Saves: Fort +3, Ref +0, Will +0
• Abilities: Str —, Dex 10, Con 10, Int —, Wis 10, Cha 10
• Skills: Listen +6, Spot +6
• Feats: Alertness

A “minor swarm” is a swarm of creatures that is not particularly threatening. Usually composed of non-poisonous, non-diseased arachnids, insects, and small mammals, they could conceivably also be a flock of small birds or a school of small fish. The point is, even en masse they’re not particularly dangerous. A minor swarm is only called when in an environment that absolutely does not have anything scarier; they are a default option just to make call swarm (almost) always get you something. They can be used for scouting or distraction purposes.

The speed of a minor swarm is always 25 ft., but it may be climbing, flying, land-based, or swimming depending on the creature.

Distraction (Ex)

Any living creature that begins its turn with a swarm in its space must succeed on a DC 10 Fortitude save or be nauseated for 1 round. The save DC is Constitution-based.