She was my best magic caster outside of the main PC.
Nobody said otherwise. But the fact of the matter is, raw damage doesn't give you as much of an advantage in battle in P3 as does other forms of support, which is why other characters are better. Mitsuru ONLY has high powered magic and healing going for her, while every other character has multiple other forms of support that Mitsuru can't provide. Plus, in the old AI-controlled combat, you couldn't really trust her to not randomly start casting Tentarafoo, which generally put you at a disadvantage.
Probably this time I won't use my usual party (Which was MC, Yukari, Mitsuru and Aikihiko), and although I'll still take Yukari despite her weaknesses (her healing is still too good), I'm unsure who to take for my other 2. I remember using Aigis and liking her my last game.