I understand you have now source code. Could you add fullscreen mode and modify flash file so it is suited to panoramic (16:9/16:10) screens? Also adding powerups like fireflower and other p-ups from mario games other than 64/sunshine would be great.
I found a bug: Rarely, when you touch that electric things on the walls, instead of you being electrocuted game just freezes (music's still playing though). It's very rare though, played it for 3 hours straight now if not more and only got it 2 times
AI changes position in last moment. That's just mean. Perhaps make it so if red balls (yellow needs to move as they give points and are supposed to be hard to catch) are within certain distance from player they stop moving horizontally?
If you make sequel, please make several missions. It's cool as it is, but would love more of it. At least 5-6 missions. Also level editor would be cool idea - basically you place objects and enemies in several rooms.