What are tiers?
Tiers are a ranking of how "powerful and/or versatile" the various 3.5 base classes are, with low numbered tiers being considered more capable than high numbered tiers. It's important to remember that certain caveats apply to the rankings:
- Tiers assume similar levels of optimization. Someone playing an optimized "weak" class (like a fighter) and using its abilities well may be a lot more effective than a poorly built wizard played by someone who doesn't know how to make use of its options.
- Tiers attempt to describe power over levels 1-20. Classes will generally be in their listed tiers immediately, though the gaps between tiers tend to be a bit smaller at lower levels.
- Tiers are based on published material only. Homebrew and house rules can and will modify the rankings of some classes or even just negate the entire ranking system.
- Tiers are based on relatively high-magic games. In a low-magic setting the rankings will be mostly the same, but the gaps between tiers will get a lot bigger, because magic items tend to be the best way for less powerful classes to cover up their weak spots.
- Tiers look at characters' ability to solve problems of any sort, not just combat.
We frown on link-only answers, so I'll go ahead and summarize the full tier list of all published classes, originally from here. Fuller descriptions of why each class is in its tier can be found here.
Wizard, Cleric, Druid, Archivist, Artificer, Erudite (Spell to Power variant) — Can do anything and everything, often better than lower-tier classes that supposedly specialize in that thing.
Sorcerer, Favored Soul, Psion, Binder (w/ online vestiges), Erudite — As powerful as tier 1, but no one build can do everything.
Beguiler, Dread Necromancer, Crusader, Bard, Swordsage, Binder, Ranger (Wildshape variant), Duskblade, Factotum, Warblade, Psychic Warrior, Incarnate, Totemist — Good at one thing & useful outside that, or moderately useful at most things.
Rogue, Barbarian, Warlock, Warmage, Scout, Ranger, Hexblade, Adept, Spellthief, Marshal, Fighter (Zhentarium variant) — Good at one thing but useless at everything else, or mediocre at many things.
Fighter, Monk, Ninja (both CA & Rokugan versions), Healer, Swashbuckler, Soulknife, Expert, OA Samurai, Paladin, Knight, CW Samurai (with Imperious Command), Soulborn — Good at one rarely applicable thing, or mediocre at one thing, or simply too unfocused.
CW Samurai, Aristocrat, Warrior, Commoner — Objectively worse at their specialty than another (often Tier 5) class, without anything else to show for it.
Truenamer — Apparently received no actual playtesting, mechanics as written simply don't work. See this question for more details.
Outside of the Wizard's saves, the consideration of the spellbook (as some DM's may have restrictions on buying your book as you become a wizard), and the character's history and background, there is no real advantage to choosing Wizard at first level if multiclassing as a fighter.
The fighter would lose heavy armor proficiency if multiclassed in to, and a high Con save has serious advantages, as you pointed out. The weapon proficiencies are a nice addition depending on character concept, but that is something you gain regardless of whether you take it at 1st level or not.
As for the cleric, they gain the armor proficiency regardless of what level if you choose an appropriate domain, they gain spells, and they promote normal spell progression. Overall, mechanically, I would say that Cleric is the stronger option. They aren't likely to do as much damage with weapons, but access to Cure Wounds and similar spells that are normally barred from Wizards is certainly a huge bonus.
If cleric is chosen, the choice of which class to take first isn't nearly as clear, nor is it as important.
Ultimately, look at the class features of fighter and cleric to decide which one you think is better for your goals. If you choose Fighter, it is advantageous to take it at first level. If you choose Cleric, it isn't really important which you take first.
A bard is not constrained by alignment.
A Bard can be as sneaky and evil as you want them to be. The limit is only found in what you try to pull off. You might want to re-examine your assumptions about the Bard class.
A Lore Bard
At level 3, choosing Lore Bard complements a spell-heavy / information-heavy approach to your Svengali/Rasputin influence peddler and manipulator. Spells and social skills combine to provide you with choices in how to influence a given situation.
How do I influence or control others?
Some good early spell choices include but are not limited to:
2d level spells: Crown of Madness, Detect Thoughts, Suggestion, Enhance Ability, and Enthrall
The above menu of spells is thematic, based on getting others to do what you want them to do, or, to at least confuse and befuddle them. The spells are not aimed at causing maximum damage, which you leave to the rest of the party. Your role is to confuse and befuddle your enemies, or avoid fighting at all due to your ability to baffle them with BS.
The Lore Bard feature Cutting Words gives you greater chances for success. It lets you use your reaction to expend a Bardic Inspiration point and influence another creature's die roll. (At 14th level, Peerless Skill helps you succeed at a given ability check). Since you are in a pass / fail mode with most social skills, and spells, that influence what people see and believe, every bonus you can give yourself is one you that you should apply.
Skills (the tyranny of choice)
You get three skills as a Bard to begin with. No matter what your background is I would recommend Persuasion, Deception, and Performance to be locked in. If you begin as a half elf, you will get more two more skills to start with. Choose proficiency in Sleight of Hand, Perception, and Insight as soon as you can manage, though Investigation might be the better choice in an urban campaign.
When Expertise arrives at 3rd level, you double your proficiency score for two skills. I'd go with Persuasion and Deception as the default. Depending on your campaign, and how often you are using your music to sway and move groups of people, Performance might be a better choice. Getting the audience/crowd on your side can make or break a tense situation.
Evil intentions? While Deception and Persuasion are your core skills, using Investigation, Insight, Arcana, History and Sleight of Hand all aim toward getting information.
Information provides you with an edge. Exploit that edge mercilessly.
For an exhaustive look at the Bard as both con artist and party face, there is a well presented guide here at a well known D&D forum that is far more in depth than this answer.
Charisma, Dexterity, and Constitution are each important, but consider where you want your mental skills to round out.
Wisdom, to boost Perception and Insight attempts, or
Intelligence to boost Investigation, History and/or Arcana checks.
Repeated for emphasis: a key currency for your character is information, that you use and abuse for your own ends. (Muahahahahahaha!)
The Bard needs high Charisma regardless of any other choices. It's the class spell casting ability, as well as where bonuses for social interaction are centered, and is critical to making the most of your spell DC's. Mind control and mind influence is in a lot of cases pass/fail, so you want to give yourself the edge when you cast a spell to influence others.
TO leverage a Bard's natural talents, a background as Charlatan (skills from this are Deception and Sleight of Hand) or Entertainer (Acrobatics and Performance skills). These background choices free you up to select others from the class skill list.
Acrobatics is something you'll probably need to survive in the dangerous world of adventuring, and sometimes entertain. (Hey, look over here the bard is doing back flips ... while the Rogue picks pockets).
Back by popular demand is a feature of the Entertainer background that will ensure that you always have room and board, and sets up situations that can lead to making contacts. You don't have to be of good alignment (just appear that way when necessary) to exploit these advantages, just talented. Information, and personal contacts: what devious mastermind doesn't make the most of both of those?
As you progress in levels, once you boost your Charisma, you may wish to consider the feat Actor (PHB, p. 165). It gives you advantage on Deception and Performance checks when you are trying to pass yourself off as someone else. That's equivalent to a +5 bonus, roughly, and makes infiltration far more likely to succeed.
An evil, devious, manipulative Bard? That role leaps off of the pages of the PHB.
This advice is campaign dependent
Experiential Note: our first 5e group featured a half-elf Lore Bard whose alignment was not good (and it got worse due to a cursed item). He was pretty effective, though he occasionally got us all into a lot of trouble. (That's fun too, getting out of trouble). Contra to the guide I linked to, which advocates using Intimidation, he didn't go for intimidation at all (leaving that sort of thing up to our Dwarf Paladin) but went for a softer sell: persuasion/deception. It worked pretty well.
Another Bard approach: College of Whispers
Now that Xanathar's Guide To Everything has come out, the Bard's College of Whispers bard school might fit your needs as well as a Lore Bard. While the general Bard class will do you just fine for levels 1 and 2, some of your requirements for being malicious fit the College of Whispers like a glove ... once you choose that college at third level.
Psychic blades provide psychic damage;
Words of Terror puts fear into people.
Mantle of Whispers (at 6) lets you kill someone and then put on their appearance for an hour (what better way to get away with murder?)
Shadow Lore (at 14) is "blackmail in a magic bag" that you can use to influence someone.