they are both EXACTLY THE SAME. they WILL have the exact same homebrew support and they will have the exact same menu, there's actually a simple hack that you can do to convert your R4 to and M3 and vice versa:
http://gbatemp.net/index.php?showtopic=41723
as for which will have faster firmware updates, I'm pretty sure that the R4 team is the one that's releasing the M3 Simply's firmware, so I'm betting that the R4 is the one that's always gonna get updated first, then the M3 with the exact same features.
So digital sin, currently they have the same/equal homebrew support? One more question aren't/wouldnt the homebrew developers focus more on the M3S on homebrew than R4 since its new in the flashcart business?