When Cait Sith sacrifices himself at the Temple of the Ancients, you'll see Cait Sith v2 appearing while Cloud is having a meltdown and he's beating up Aerith. I can see the point of removing his appearance there, but now, you don't see Cait v2 appearing anywhere. So when you wake up in Gongaga and can add Cait Sith back to the party with PHS, it feels weird, since you're like, "Wasn't his body destroyed? Why can you add him back to the party as if nothing happened?" My suggestion would be to have your party members appear in the village part of Gongaga, including Cait Sith, and when you talk to him, he says he's the next version of Cait. This way, you'll get the feeling that the game acknowledges that he's back, and lets the gamer know that he can be readded to the party.
Same for Aerith's death scene if you manage to save her. After Disc 1 ends, you can add Aerith back to the party, and she'll fight along as if nothing happened, even though a while ago, she was unconscious after the Jenova battle. Cloud and Aerith never have a "Are you okay? I thought you were a goner for a while" conversation later in the game. Would it be possible for Cloud and Aerith to have some kind of dialogue before leaving the Forgotten Capital? Maybe when Sephiroth tells Cloud to go North, Aerith could catch up with the party and say something. Cloud could go like, "You almost died! I can't risk you coming along, it's too dangerous!", with Aerith responding something like, "Oh, shut it. I'm alright, let's go!" This lets the player know Aerith is okay now, and can be added to the party again.