I've never used a GBA emulator on my 3DS before, but I do have a few GBA VC injections and I definitely agree with the injections being a very good choice. Fire Emblem runs fine, a few Pokémon ROM hacks (Light Platinum and Theta Emerald EX) run well, too. Haven't tested a vanilla Pokémon game, though, but if ROM hacks work, then games like Ruby and Sapphire and Emerald should work. Even Super Mario Advance 4 works fine after messing around a bit to get it working, though it does have a "Save Data is corrupted" nag screen whenever I boot it up. Save file is totally fine in reality, though.
If you're willing to put in a bit of extra work to make GBA injections, those will do just fine if you don't care for save states or cheats. If I heard correctly on the forums, some users have said that the 3DS has actual GBA hardware, apparently, so it should be very accurate.
As for CFW, there is the Seedminer method, which I used, but I have no experience with a flashcart, so you could check to see if your SuperCard Two is on the list for the NTRBoot method in the 3DS guide.