Pretty cool concept. My only issues are:
1. There are no sound effects. i would recommend using FX Hammer (here's a cool tutorial for using it) to make them, as the sounds turn out more cleaner, and usually sound more retro.
2. The recorded music is really annoying I recommend that you download MIDI files of the og soundtrack, then copy the notes down. It's tedious, but I think the result is super cool, and worth it! Or maybe somebody else already made the .uge files, or a famitracker remix you can copy.
3. I feel like the controls are a bit strange, but i understand if it's a bit too difficult to change.
Otherwise, the artwork looks amazing, and Sonic looks super awesome! I think if you can learn how to animate the flowers and water, this will become a good sonic gbc port.