The endings you see by beating the game 'normally' change minimally depending on how you beat it. The fun part is starting a New Game+ and beating Lavos at several different points during the story line to get some completely off the wall endings. (The best one is if you beat him as solo Crono right at the start of the game, or beat him when he emerges in zeal)

I'm guessing the anime parts don't change, but I have only ever beaten the game once on a non-SNES iteration.

Aside: Come to think of it, when you fight him in Zeal the shell is the really overpowered part. If you killed the shell first via the End of Time bucket, ported out, then did the story sequence and skipped the first phase it would probably be an easy way to get that ending. Has anyone tried this? (I know spawning him in zeal with his head cut off works, I just can't remember if the rest of him is normal strength and if iit still triggers the *ending name*developer's ending