Since the next version was brought up, I'd like to make a few suggestions on things you could do!
-Please give us the ability to bench Cloud after Midgar (and please don't force him into the final battle/Dark Cave sidequest). Letting us permanently bench Cloud for the entire game (save for the City of the Ancients, and the Northern Crater, both in Disc 2, and in Disc 3 to avoid a glitch found there) would vastly improve replayability since we could play with the parties we want during the main game instead of having to wait until the end of the game.
-If you haven't decided on an Innate Skill for Yuffie yet, maybe she could have one that has her randomly following-up an ally's attack with an attack of her own, or randomly repeating a spell casted by an ally? It could be called something like "Copycat." I think it'd fit with the whole Ninja theme and her personality.
-Is there room to give the Aero spell line to the player? Chocobuckle is a kinda sucky spell, and Tornado is only available near the end of the game, leaving Mages high and dry on hitting Wind weaknesses for a very long time.
-I've already mentioned this a couple times, but would you please consider buffing Red's Stardust Ray limit? It barely does half of what Earth Rave is capable of doing.
-Unless you change the stealing formula to use the Dexterity stat to determine success, would you please have Yuffie come with a Sneak Glove upon joining? Largely for convenience's sake, but it would also make stealing much more possible in Arranged Mode (if you plan on keeping enemies at higher levels on Arranged Mode).
-I went back and beat Zack in Normal Mode, but since Cloud has been nothing but dead weight, I cheesed it with W-Summon KotR. Please either nerf the Zack fight, buff Cloud a bit, or both.
-Since the Hero's Medal currently does nothing, maybe you could make a new Superboss that puts even the most optimized party at Lv.99 to the hardest test and have the Hero's Medal unlock said Superboss? There isn't really much to challenge you once you hit Lv.99 and get your hands on some fun Materia like MP Turbo, Quadra-Cast, Mega All, and Multi-Cut, so having a boss that's legitimately challenging even with all that would be fantastic, in my opinion.
That's about all I could think of. I hope these suggestions help you decide on things to add for version 2.0