@Absolute_Justice: It would be unique, to say the very least. Sounds interesting, especially if you would add the personality or general backstory.
I actually have a few ideas and can't settle for one as my 3rd.
First would be based off Kama from Omega Complex, hero neutral, the gunslinger i was talking about.
Next, based off Relius Clover from Blazblue, villain neutral, scientist and high ranking officer of UOS.
Last would be Touko Aozaki from Kara no Kyoukai, neutral, more or less like the Relius idea, a scientist, weapon dealer and puppet maker, just not with the UOS (i might even consider including one of them as a NPC for the other).
I actually got many more minor idea, but all of them will probably wait as i'll stick with two chars for now.