If stat progression doesn't matter, then what makes Aeris worse than anyone else? At that point it all comes down to weapons, and as mentioned, she gets her best one early. Obviously stats matter, otherwise her physical attacks with that weapon would be as good as everyone Cloud's.
Yes, Cid is great, not only because of Highwind though, because that's a skill you'll use on a handful of enemies in a 60 hour game. One can't just look at the endgame like that, otherwise no one is useful except Barret, Cid, Cloud and Tifa, with Yuffie occasionally chipping in for Morph. Which granted, is how some people play.
Also, the whole game's easy enough that it doesn't matter. Even Emerald and Ruby, with a solid setup, can be beaten in very short order (with KotR's animation taking far more time than the actual fight).
Aeris gets something no one else does, in Invincibility for the whole team. Even dropping damage to 1/255 can't recreate that effect, and assuming it was possible, she'd be the best KotR user in the game, with around 200-400 less HP than the tanks, and good natural magic resistance. None of that matters in the long run, but just because you don't use her, doesn't make her useless.
In the original release, she was also the best magic tank in the game. Doesn't mean much, but she can get some use out of that. Anyone can use Beta and Trine, but she's still best at it, just like anyone can attack.