I've read that the graphics are improved *slightly*. I read that they added bloom lighting to MP1, although I can't verify this because I don't know what bloom lighting is. To me, the graphics look the same as the original. That's fine with me though because I always thought MP3 looked the same as MP1 anyway (this isn't a knock on the game, they look great).
Apparently they've also modified some of the boss battles to make them more fair and balanced.
They also added achievements to MP1 and 2. I don't know what you can do with them, but when you beat a boss, the Samus "S" pops on the screen and it says "You have defeated <name of boss>".
Plus, the box is badass.