Oh, I forgot to post the finalised list of innates:
-) Cloud: The copy thing took a tonne of space and was causing mass confusion due to it also copying the name of the character when listing the trigger (so it was tough to follow who had what). Instead, he now has a chance to get a Fortify stack that boosts his level when he takes magical damage/effects.
-) Barret: Same as before; defensive stacks when hit in the back row, strength stacks when he's in the front row with both overriding each other.
-) Tifa: Whenever the Sense command is used by any character, she gets a one-off boost to STR called a Focus stack. Originally, the idea was going to be spacing these out into multiple stacks and using something like the Defend command instead but I had trouble getting it to recognise when she used the command, rather than just anybody, which derailed it a bit.
-) Aeris: Slowly regenerates MP, 1 MP per 'tick'.
-) Red XIII: Slowly builds Strength and Magic over time (similar to the Behemoth enemy in NT), but loses these stacks if KO'd.
-) Yuffie: When hit by a physical attack, has a chance to raise physical evasion to 255%; this effect is lost if she is hit by any magical attack/effect.
-) Cait Sith: Rage system made it into the final build. Use the Morph command on Cait Sith when he is under one of these four statuses:
Poison: Absorbs Poison (poison ticks will heal him too), will use Bio2 on all opponents.
Fury: Gains Barrier, will start to use 2x-Cut on random targets
Silence: Attack & Magic set to 10, will start to use Mime command
Sadness: Gains MBarrier, will attack a random target and then Defend
-) Vincent: Will nullify Fire, Bolt, and Poison; also starts each battle with the Death Force status.
-) Cid: When in critical HP, and hit by a physical attack, Cid's Luck stat will double one time.
Edit:
also just fought a random battle in train graveyard with 2 hounds, killed one hound and the battle ended
Sounds odd; I think I changed the name of those graveyard enemies (I replaced the Sweeper there with a 'junked' version) but I can't recall if I did something to the formation or AI as well. I'll have a look.
Edit 2: Fought the encounter and checked the formation/AI but didn't see anything out of place. Are you playing on Arrange?