After messing around with the newest SVN, I found a fix for the messed up character textures that was plaguing Megaman X - Command Mission.
Perviously, you could turn off the VU0rec/VU1rec CPU options to fix the textures, but this caused PCSX2 to run as slow as a slideshow. I just discovered that turning on VU0rec/VU1rec alongside the new MicroVU0/MicroVU1 options fixes the textures without the slowdown.
I was using the SVN build of the GSDX plugin (1873) in DX10 hardware mode.
Reference thread:
http://forums.ngemu.com/pcsx2-forum...black-triangles-scatters-over-characters.html