The thing is, they wern't re-inventing the weel. They took a look at the Adventure games, mashed them up, wrote a shittier story, and rushed it out the door.
Hmm... considering that you're using sprites from the portable games, how about remakes of the Game Gear, Advance, and Rush levels? So that you could make something different for a Generations fan game.
If I recall correctly, the Japanese manuals for Sonic 1-3K stated that each island had it's own set of Emeralds. But the current cannon (if you can call it that at this point) since Adventure had only a set seven of them.
Cool sprite, but the thing that bugged me about Sonic 2 and 3's sprites was that shiny dot on the side of the head. It made Sonic and co. look like they were made of plastic.