The Trilogy has new controls, supposedly a more clear story in Prime 1 and possibly more voice acting. Better textures. Faster loading times. Oh, and supposedly a lot of the battles and bosses are much harder because the speed has been amped up considerably. Also as stated before, some of the glitches and freezes resulting from sequence breaking have been fixed.
I have no objection to more Metroid games, especially a remake of Metroid II, a prequel to zero mission or a sequel to fusion. I just feel like the Phazon story has been resolved and doesn't need to be revisited.