ReGBA - (buttons are mapped incorrectly/can't change, not a lot of settings options and menu screen still flickers
It's gpSP that has few menu options and had the incorrect button mapping, that has been fixed, reGBA's buttons are fine and freely mappable and it has many more options however the menu screen still flickers.
Compatibility is the big problem. For the reGBA off the top of my head, Kirby Nightmare in Dream Land, Lufia: the ruins of Relore and Steel Empire crash on startup, Aladdin and the Iridion games shortly after.
For gpSP Donkey Kong Country 3 won't run, nether will Steel Empire, Aladdin crashes shortly after launch, for glitches Kirby Nightmare in Dream Land secret levels won't unlock until you leave a world and come back and the water level in Crash runs really, really slow.
In both reGBA and gpSP in the game Super Mario Bros 3 Piranah Plants are invisible under water, specifically in World 6-6.
Also for SNES9x4D and Pocket SNES games with the SA1 and FX Chips are slow.