When I think of 'acceptable' emulation, I think in terms of framerate, controls and rendering. Cheating, save editing, filters, these are extras. To say that a method for playing a game is unacceptable because you can't cheat is rediculous in my opinion. VC injection is by far the best method for playing gba roms on 3ds, and will be for a long time. If you really need to cheat in order to enjoy these games, maybe you should look into ram editing vc games with spider/skater.
Edit, also, if I'm not mistaken, some gba roms were hacked to include a custom intro that was essentially a trainer. Perhaps injecting these instead of a clean rom.
doing simple boring ram editing is possible with skater/spider/ntr, doing actual fun stuff with cheat stuff is significantly different.
Framerate is important, rendering is important, savestates are extremely important. I'd rather have fast forward than savestates but not by a wide margin.
Filters are ugly and bad.