Honestly the cutscenes could make perfect sense if she were to be revived after the fact when you revisit the temple of the ancients.An explainable revival would be allowing you to find the holy materia in the temple of the ancients and using it to revive Aeris in order to fight Sephiroth. Iirc there wasn't anything solidifying her death AFTER that scene, 3D cutscene wise, except for maybe the very end, but all that was, honestly was just a throwback to the very first cutscene of the game and could be explained any number of ways if you wanted to hack it.The final battle where Cloud uses Omnislash could be replaced by Cloud and Aeris being in the party. Aeris using Holy, with a random graphical effect, maybe Ultima, but instead it deals 9999 damage to herself and Sephiroth as well, making the ending make total sense as long as a scene with her beforehand talking about doing what needs to be done to save the planet is added. The third disk should have plenty of room for a few extra scenes I'd think. That random Omnislash honestly made no sense anyways to me. As for explaining both the use of holy to revive Aeris as well as her using holy at the end(for the example I just made up), you could just make the holy materia her new limit break item, which makes her final limit break "Holy" instead.