It's really nice initiative, because of multitude config options, but all the SNES emulators in the bundle tested by me had noticable slowdowns on my n3ds and sound errors such as cracks, with used game.
The game I've tested is custom patched JP DQ I-II for snes (added translation to it).
I used initially this option because it wasn't booting on normal VC. Normally it only worked on the: pocketsnes, catsfcs plus, as the game wasnt working on VC it didn't work on the "Snes9x Next" either.
Later I found a way to run this custom patched rom on the VC - all I had to do was to remove HEADER, because patching the rom required to add to it "header". So it runs now perfectly on the VC.
After all i also tested it without header again in the Snes9x injection and it worked, but same as other emulators: slowdowns, cracks. so yeah, the VC is the most stable option for retro games by now.
Tested all of them with enabled/disabled rewind feature, so its recommended to disable it, imo. The best one for me was: PocketSnes.
I like how you can change display of bottom screen. I even made a custom one, but on the 3ds it displays whole screen highlighted in BLUE color.
When we are at it, one suggestion, it's possible to implement in the future releases, custom top screen borders/frame for the black bars (just like the ones in the super game boy) in the modes that don't stretch to the full screen?