Your predicament is a pretty common one, and applies to any GM who has a player focused on summoning monsters. Even without the brokenness that is Master Summoner, summoning-focused characters can quickly break the action economy and make it so the rest of the group has little to do, most of the time. That said, here are a few things that you can do to reduce the power of your Master Summoner player without removing his flavour. There are basically two things to do here: carefully limit the creatures that Summon Monster is capable of summoning, and make the Master Summoner's resources matter more.
Don't add monsters to the Summon Monster list without careful consideration
The list of monsters that you can summon with Summon Monster is reasonably well-balanced as it is. However, there are a bunch of unstated assumptions that it has that can cause some serious problems if they aren't adhered to. Some of your problems come from this.
Ban Summon Good Monster
That feat is really super powerful, especially at lower levels. It gives you way more battlefield control options than you would normally get, as you have already noted. Most of the monsters on that list are fine, but no one is going to summon the well-balanced monsters off a list like that, they're going to summon the awesome, way-too-powerful ones. If you don't want to ban this list outright, then at least go through it with a fine-tooth comb and assure that the abilities that you get from it at a particular level aren't out of line with what you get from the normal list. For example, the first creatures that have any abilities that are either ranged or spells are in the Summon Monster 3 list, and those creatures are pretty terrible is a stand up fight (Dretch and Lantern Archon).
Ban non-standard Elementals
This is similar to the point above. When Summon Monster was first written, there were 4 elementals: Fire, Water, Earth, Air. Each of them is an effective tank in their environment, and are reasonably well-balanced. Allowing the player to summon the other 8 types of elementals that have been added since is adding to his versatility by a significant amount, and versatility equals power. As you've noted, some of the additional elementals have abilities out of line with what the normal elementals have. You don't have to allow the player to summon more powerful monsters (like the Mud Elemental) if it's going to mess up your game.
Keep the general Summon Monster guidelines in mind when adding new monsters
To sort of go back on what I said above, there's nothing wrong with letting your player have more or different creatures to summon, as long as you're careful about what these new creatures give the player at that level. Make sure you look carefully at what a particular level of Summon Monster gives you before adding new things to that level. For example, with Summon Monster 2, you have the following roles: melee ground tank (most of them), flying tank (air elemental), swimming tank (water elemental, octopus, squid), high damage/poison tank (fire elemental, giant centipede, giant spider). The only battlefield control options available to any of these creatures are the normal combat maneuvers, mainly grapple and trip. None of them have more powerful control options like the faun or mud elemental do. This extends through most of the levels of Summon Monster. For example, nothing below Summon Monster 9 has the ability to cast spells like a PC.
The final arbiter of what the player is allowed to summon or not is you, as the GM. If you think that a particular form is out of line for the power that a level of Summon Monster gives, then you are well within your rights to ban that form, or put it on a different level of Summon Monster. It doesn't matter if the rules say that the player can summon a particular monster; if using a particular summon is going to make the game less fun, then that summon should be banned, or otherwise limited.
Make the Master Summoner's resources matter.
The standard game rules make some assumptions about the kind of game that you're playing, and tune player resources based on these assumptions. The game assumes that the average player is going to have 4 encounters in an average day. For a Master Summoner with 18 Charisma, that means that they can summon 2 monsters in each encounter, and 3 in one of them. Adding 2 monsters to a fight is something that can be worked around, in general. If you have significantly fewer encounters, then you need to figure out a way to make your player's resources matter again.
Intelligent enemies should have intelligent protections.
For example: Any intelligent enemy that knows about the summoner is going to have a Protection from Good ready to go (whether from a potion, and item, a scroll, or a spell prepared, depending on the enemy). Protection from Good doesn't shut down your player entirely, but it does make it so he needs to use more of his Summon Monster abilities in a single combat to remain effective. Spellcasters can use Dispel Magic to quickly end a summon. More prepared enemies can use Magic Circle instead of Protection, which is a little more effective.
Reduce the number of summoned monsters at once.
Like you say at the end of your question, you might consider limiting the number of monsters summoned to two spells. The player could use one eidolon and one Summon Monster spell, or two Summon Monster spells, but no more. This means that the player can basically use the same number of Summon Monster spells that he could normally use per encounter in a 4-encounter-per-day game. You might allow the player to use extra uses of the ability to get more monsters at a time, to make the player feel like those extra uses are still useful. For example, maybe the first 2 castings take one use each, but any after that take 3 each.
Reduce the number of uses per day.
If your campaign requires only one or two encounters per day, then it might be helpful to reduce the number of Summon Monster uses that your player gets directly. In a 2 encounter per day game, reducing the number of uses to 5 or 6 would likely be helpful. This might make your player feel shafted, so it might not be the best thing to do.
Use more numerous monsters, or ranged monsters.
Basically, alter your encounter design to take the summoner into account. If there are a dozen orcs charging in that will likely overwhelm the party, the summoner can deal with them while the party deals with the rest of the encounter. Alternately, powerful ranged monsters can target your summoner, making it a priority for the summoner to send minions to deal with that threat while the other players take out the main encounter.
The Ethereal Plane is another dimension, described in more detail on Pages 48 and 49 of the DMG. It may help you to replace the term "plane" with "dimension." The ethereal plane borders several other planes, and is often described as a muted, foggy outline of whatever exists on the plane that it borders.
So, take for example that you are in a corridor inside of Castle Ravenloft. There is a spot in the ethereal plane which looks exactly the same as the castle corridor, except it's all fuzzy looking and grey and foggy. Any creature on the ethereal plane is invisible to the stuff in the castle corridor, but the creatures in the corridor are visible to the ethereal denizens. Creatures on the ethereal plane also feel no gravity, and can move through walls easily.
The ethereal plane is used very often then for travel, as well as espionage, since travelers can move through walls, as well as spy on people on the material plane without worry of being discovered. Ghosts and other such incorporial undead can move into this plane at will (which is what allows them to turn invisible).
If a character can use true sight, they can see into this plane. So if anything is spying on them using this plane, they will see it. They can also see ghosts and other such spirits that try to hide from them by moving into this plane. They will also see things that were hidden in the ethereal plane for safe keeping.
As for the effect of this on your campign, that really depends on how much you use alternate dimensions as a DM. If you don't use the ethereal plane for very much, the spell just means that the PC can follow ghosts and other such things, as you have noted. If you like to put spies in there, or other such hidden things "stashed away in the fourth dimension", then the PCs will notice those things. The effect is pretty minimal, since your players would acctually have to shift themselves into the ethereal plane in order to affect anything you put on that plane.
As noted by Andrewk, Ravenloft is filled to the brim with trapped ghosts. Even if they don't directly interact with the players, it can be a powerful narrative/aesthetic device for the PCs to see so many souls in the ethereal plane as they move through the castle.
Best Answer
Dire Bats have blindsense, not echolocation
The statblock for the Dire Bat lists only Blindsense, not echolocation.
When playing a game like pathfinder, you have to make some allowances for the system to work. Stats, turns, and actions are a simplification (with sometimes ridiculous implications) of real-word scenarios.
Thus, when it comes to creatures (especially in combat, which can already drag on) it's best to trust the stat block implicitly. This serves a few purposes
It saves non-experts from having to do research: If the GM isn't an expert on bats, then all he needs to do is know the keywords used on the stat block and he's good to go. Something like a bat is one thing (most people are aware of echolocation at this point), but when it comes to Green Slime knowing whether the creature is completely immobile or not is obscure trivia, and could start a table argument. For the purposes of combat, it's best to trust the statblock and agree that the slime isn't going anywhere, and the bat can see in any condition.
It could affect balance: Sometimes stats don't make a ton of sense. Why does damage for some weapons change between some editions of D&D, but not other weapons? Did steel get less sharp and more pointy? Rather than explore minutiae it's generally best to trust the designers of the system that they made things the way they are. If you start worrying about how rain, snow, sleet, dust, and fog affect echolocating creatures different you could wind up inadvertantly making bats weaker than intended (after all, there are a lot of ways to conjure up some of those things, and some aren't even magical).
Besides...
In the real world we're not really sure if storms mess with echolocation in the first place
We know that bats don't like to be out in the rain, but we're not entirely sure why. There's been some research done, but due to limitations in the equipment used they were unable to test echolocation hypotheses. The researchers did determine that the caloric cost of flying as a wet bat vs a dry one was around twice as high, which would be a serious factor, but aside from wind-levels pathfinder doesn't try to address adverse weather conditions much in Flight, and certainly doesn't model the difference between how rain affects a Duck and a Bat very well.