Any Slot-1 or Slot-2 is fine (bear in mind that Slot-2 cards require some sort of PassMe method), just don't buy an Acekard RPG!! They have absolutely no homebrew support and are a bad way to go. I recommend the R4, but if you're also wanting to play ROMs, look into the CycloDS as well.
wtf!? lol. how would you know? RPG has run all dldi homebrew i've thrown at it (with auto dldi patching), except for dslinux. Indeed i assume it has at least equal compatability with R4.
If homebrew is your only call, not roms, and you want to be able to play the really old homebrew, you'll need a slot two cart and passme, like supercard/gbamp i think.
however there isn't alot of older homebrew of high quality, given that development libraries and projects have improved significantly over time. so a slot one might be easiest and best after all (with the added bonus of auto dldi patching, although supercard slot2 has it too).
M3 Real probably works fine with homebrew, but it's not exactly the most convenient with it. You can't see custom homebrew icons (Like the commercial games have) and they must be on root. I haven't heard of any problem with moonshell running, but also it should be noted moonshell is better imo than media-extend, the outdated built in player (which is based on old moonshell)