I agree that controller support is not optimal right now.Firstly, congrats on the full launch for Sonic 3 A.I.R. I was already intrigued by the project when I first saw it here and I'm glad that you were able to do the entirety of Sonic 3 & Knuckles since then.
It has honestly given me a better appreciation for Sonic 3 & Knuckles that nether the original or even Sonic 3 Complete could do for me after revisiting the game via A.I.R.
The only suggestions I could make are more for the controller support that's currently in it, as I think it would be nice if there were options to rebind the buttons on your controller for either those who don't use a XB360/XBOne pad or for people who want to customise the button mappings to their preferred liking, along with some sort of auto-detect system that some other games use in case your controller gets disconnected mid-way through and you want to hook it back up without having to restart the game.
Other than that minor suggestion, great job on this project and I wish you the best of luck with your future projects.
Actually (in my defense ), both button mapping and rescan of controllers is possible - but both is kind of cumbersome: Remapping buttons requires editing a JSON file, and rescan can only be done manually with the F3 key.
So we need some improvement here.
I'm having plans for including a controller config menu, which will certainly be helpful. And the auto-detection would be neat - I'll have to check first if there's downsides to regularly checking the controllers, but if not, this will get added as well.