Could it also be 4 way vs 8 way controller? I read 8 way controllers on these games can have glitches when transitioning....it could manifest as control delays. I happen to have a 4 way plus an 8 way setup so I always use 4 way for the old games.
@IanDaemon i found that when I'm in game and I bring up the retroarch menu, I can't move anything in the UI. The cursor will not move with keyboard or controller. I'm stuck there until I hard reset the pi because I have no input. I thought about a reinstall but I spent a lot of time scraping and setting up and I'd hate to have to do it all again.
There must be something wrong in your setup. RetroPie on a raspi3 with decent peripherals can run smoothly any game from the 8/16-bit era without any tweak. Just install, config input, put your ROMs and play.
[Footnote: OK, maybe 3D games, like StarFox (SNES) and Virtua Racing (Mega Drive), can stutter a bit. But the games you mentioned should work just fine.]
The higher the speed, the better it displays, but anything above 27000000 f'd up the colors badly for me.
Definitely playable for anyone wanting to use this screen, but it still drops some frames, mainly during cinematics and stuff. Personally, Gonna try out a 5" HDMI screen, don't wanna compromise on the gaming experience too much.