I won't go into too much detail for the Gene Gadget/Panic Puppet clearing problems since so many do make note of the issue, but it still is a major issue. GG and PP don't have the requirements to 100% the stages and in the case of Panic Puppet finish the game. Either adding Tails and Knuckles or giving the last Chaos Emerald at the end of the PP boss would allieviate the latter problem, but several medals will need to be implemented.
On the topic of bosses, one persistant issue I found myself running into constantly was the ring loss I faced with getting hit. In places like the boss fights, I'm able to recover a scarce amount of rings if any by the time I've landed from my hit. An extra two seconds to the bounce of the rings would fix this problem greatly. Also, the hit boxes of the PP Boss Trio are very awkward to hit still.