I found out how to make the boss characters (G666/DA) selectable on the character select screen yesterday, and PM'd the instructions to Lord Phrozen to use whenever he updates his trainer next.
If you know how to use a debugger, the following things need to be changed:
0040958D: MOV EAX,19
00409592: NOP
0040828B: NOP
0040828C: NOP
Once that is done, the sprite showing your currently selected character should change to Neco Arc Chaos instead of whoever you have selected, which prevents the game from choking and crashing when the boss characters are selected. Once that is done, place the selection cursor over Kishima and hit D to cycle between him and the boss characters in the same way that you cycle between Neco Arc Chaos and Nero.
Regarding the MBR boss characters, they don't seem to exist in MBAC as far as I can tell.