Hi Bluewoods.
I took a stroll to the NDS emulation forum after seeing the GameYob thread and saw this DSTwo-related one (outside of its assigned forum, /NDS/Flashcarts/Supercard, but meh).
SNES
As of CATSFC 1.29, many games will have been improved in speed, audio accuracy and controller synchronisation, so you can tap your buttons and it won't release them a whole second later anymore. As a corollary, you can tap your buttons and it won't miss you pressing them anymore.
1.29 also forces frames per second to be up to 20 instead of almost unrestricted / 60 FPS, because otherwise the emulator running on the DSTwo's internal processor cannot both send the screens to the DS and get the status of controls from it. It sucks, but otherwise it would skip button presses and releases like crazy.
Many games actually run at that 20 FPS, including formerly problematic ones in CATSFC "NEBSFC" 1.25 and earlier, but notable exceptions are Kirby Super Star, F-Zero, Mario Kart, Mario RPG Seven Stars, SMW2 Yoshi's Island and so on which, on a real SNES cart, include co-processors that are expensive to emulate on a DSTwo.
GBA
As of... NDSGBA 1.21 (which is the often-recommended version because of the ability to use game_config.txt to improve game compatibility, download one and put it at (microSD)/NDSGBA/game_config.txt)
Cheats are odd, the touch screen doesn't work in the menu, some games don't work despite game_config.txt being there, and there is lots of instability in the menu as well as crashing in the middle of games.
As for the controller synchronisation, I've only played Pokémon on NDSGBA 1.21 and it didn't skip buttons that much if at all; I should load a platformer on it and see how bad it is. However, currently the source code for this emulator is unavailable, and there's a sort of petition thread going on in the Supercard forum about it, so nothing can be done about this.