without the need to apply anti-piracy fixes and such manually), but for most users nds-bootstrap is probably enough.
Flash cards aren't free, but will run slightly more DS games and some would argue more easily (e.g. Compatibility is very good, but not quite as good as a flash card. Nds-bootstrap is an NDS ROM loader which patches games to load from the SD card instead of from the cartridge slot. You can find or inject your own GBA ROMs and install them to the Home Menu on a hacked 3DS. You also have no link cable support, so no multiplayer. This has excellent compatibility, discounting games with special hardware like accelerometers. The 3DS includes the hardware necessary to run GBA games natively via AGB_FIRM. You can play most of the GBA/DS/3DS library on any model of 3DS without a flash cart via soft-modding/custom firmware.