i feel like the problem you're identifying is something pretty common in action rpgs and their relatives in that era until more recently, which is that magic uses a very different kind of mechanical system than weapon attacks and the like which isn't really fleshed out in the same way. i'm inclined to think that something like secret of mana (or older than that) was kind of a big inspiration for tri-ace's games since there's a similar focus on visual effects and the "screen freeze" at spellcasting. in secret of mana though, magic is kind of akin to the weapon attacks, which also generally hit one at a time, have delays due to the stamina bar, and so on...so the gap becomes more jarring once you go to a game where some of your characters start doing fast combos and the other one pauses the game 50% of the time to hit with meteors for a few thousand damage
i definitely think it's true that star ocean 2's mages are lacking in both mechanical design and overall power level (vp's...are really good, but it's boring to cart around 3 of them and menu enemies to death) but also...not really the only part of the game that's wonky and unbalanced. but i do think it's something that a lot of designers have iterated on in time, not just tri-ace; playing spellcasters wasn't super interesting until the later ps2 era in tales games either, and ff7r's version of aerith probably has my favorite action-game type mechanics for a "mage type" i've seen. (obviously, it helps that "basic" elemental nuke spells are baked into materia in that game and designed for anyone to be able to use, so they really had to come up with cool stuff to give her.) in valkyrie profile 2 spellcasters still aren't super exciting, but they bring a bit more to the table in terms of non-damage utility and it's easier to work around their poor combo power, and the more recent star ocean games (even if i don't think i would really recommend 4 or 5 to much of anyone, lol) have at least tried to bring magic mechanics more in line with the sorts of combos and stuff that weapons have, to varying success. in 6 the healer actually still doesn't play like other characters but she has some interesting resource and buff mechanics that i think are pretty cool...
anyway, i just wanted to finish writing this before someone comes in like "tri-ace are bad at making most things amirite" or something lol. i'm still a big fan of most of their games, jank and all