I would say the best option for playing GBA on 3DS would be using Nintendo's own built-in, native GBA emulation on 3DS, as it isn't really emulation at all, and all the ROMs run perfectly. But it does have fairly robust features and customization options. But it's not perfect, and I would say it's honestly more useful for GB/GBC emulation than the GBA itself. MGBA is fairly serviceable, for the most part. I also found GBA Runner to be a pretty shoddy emulator. However, I wouldn't recommend TWiLight Menu/GBA Runner as the optimal way/emulator to play GBA games on your 3DS, simply because TWiLight Menu essentially turns your 3DS into a DS, and the DS has a pretty low screen resolution. I don't have any better advice than what has already been given on the corrupted folder/SD card front.
