I believe moonshell2.1 has rom loading on an M3i0 IIRC, but it is by using the ndslink and touchpod.nds. There is a plus to having Moonshell2 as an alternative loader (doing this for a friend xD)...you could just forgo the commercial rom loading on moonshell2 (its better to load it on Sakura anyways, what with the cheats and whatnot) and just use moonshell2 for loading the homebrew stuff using the touchpod loader. Technically this doesn't do squat apart from exchange the slowness and unsmexiness of touchpod into Moonshell2 without commercial roms, but its better than resorting to touchpod when all you need it for is homebrew (I'm guessing that is what the general populus uses it for anyhow).
And lastly, I'm obviously a Moonshell2 fan so I feel that anyone that doesn't have moonshell2 is a lost soul xD.