I had this bookmarked for a while and only just got around to reading it because it's long and I'm lazy.
Nice to see your progress, dude, always been interested in animation and animation processes despite not really having the patience for it.
I will say, though, that you can set up the "Tolerance" on Photoshop (so the fill tool, the wand tool etc) that'll branch into different hues and essentially allow you to work within anti-aliasing with those tools, which is how stuff like Skullgirls managed to keep their AA.
HochiganMeat
oh and heres the thread http://www.newgrounds.com/bbs/topic/1404977/2#bbspost25954355_post_text