Persona 3 FES Tiers
S
Main Character
Obvious reasons. He can use any weapon, and he’s the only character who can use multiple Personas. If you encounter a Shadow that can exploit your weakness, simply change your Persona. The only real weakness is your roster at any point in time…you could have a killer roster, or a weak one, but it’s always changing. Oh yeah, and Fusions…can’t forget those.
Fuuka
She’s not a fighter, but her support skills are great, especially her last one, Escape Route. No more Traesto gems. 
Being able to see the enemy’s attacks is a big plus so you can plan accordingly.
A
Aigis (The Answer)
[details=Spoiler]
She has all the perks that the MC had in The Journey, except she can only use piercing weapons. This means that you have no choice but to rely on Personas for other physical attacks. I haven’t actually checked this, but I don’t think Aigis can use Fusions. Also, not having access to the Compendium hurts. Her ranged attack when encountering enemies is great, so you should be able to get first strikes often.[/details]
Akihiko
Debuff master. Very useful against bosses, since debuff skills work on everybody. The final boss of The Journey can’t block debuffs with his annoying reflect-all skill. Would be S tier if debuffs could stack like they did in Nocturne.
Mitsuru
The only character with Tentarafoo, which can be a life-saver if it actually hits. She’s also the only character with Mind Charge, which is extremely useful because Mitsuru already does impressive ice damage. Always useful to have in boss battles if the enemy isn’t immune to ice.
B
Aigis (The Journey)
She has great support skills, and she’s the only character who’s immune to common physical attacks without the tradeoff of having major weaknesses (that’s why a Persona who might have high immunity against physical attacks will have severe weaknesses elsewhere). The major problem is that all of her attacks are physical, which means she needs constant healing. There’s also little variety in her attacks, as most of them are strikes. Also, Aigis is better against groups of enemies, making her less effective against bosses (most of whom are usually single).
Junpei
In-game, Junpei claims that he’s a “fireman,” but really, he’s more about the physical attacks. His fire ability isn’t impressive compared to Koromaru’s, but at least he has some fire attacks to use when his physical attacks aren’t working. Junpei has a variety of physical attacks which make him better to use over Aigis. After a certain event, Junpei regenerates HP which makes him even better since it covers the cost of using his physical skills. His regeneration skill will stack with any equipped item that restores HP over time.
Yukari
She’s a healer first, then a wind user second. She should usually be on support duty during boss battles unless the boss is weak against wind. Using her against the final boss in The Journey is tricky, because if you get nailed with the boss’ last resort, you might have to redo the battle again (if you reached this far, you KNOW what I’m taking about). The major problem with Yukari is her low HP, so you need to equip a vitality ring.
Koromaru
Fastest character in the game, by far. If this was Nocturne, he’d be like Matador…you couldn’t touch him. Impressive fire and darkness skills, plus two immunities and only one weakness (although it’s a big one). It’s too bad you can’t equip Koromaru with any shoes, so you’re stuck with bare paws with no special ability. Koromaru is also better vs. groups instead of single enemies. There’s no chance you’re going to hit a boss with a Mudo skill, so that’s half of Koromaru’s ability gone. In a situation like that, you’re better off with Junpei who has fire AND big damage-dealing physical attacks.
C
Ken
Weak character. Has a few good skills to use if the enemy is down, but sometimes you want the enemy to stay down in preparation for an all-out attack. His skill set is just all over the place; he has one single-target thunder skill, a few healing skills, a few single-target physical skills and some Hama skills. Don’t bother using him in boss battles…without Hama, you’re left with a sub-par fighter. Basically, the other characters are masters of the things of which Ken is only mediocre. If you want thunder, use Akihiko; if you want piercing attacks, use Yukari, Aigis, or Junpei. Ken has his Hama skills, but against a boss, he doesn’t have much to go on, except as a backup healer. In the late game, you have even less reason to use Ken, since most enemies have Mudo skills.