The bones just need to be done in a minimal yet sufficient manner. In other words, make it look good with the fewest bones possible. I would just do one bone per major body part, like one bone for the upper arm, one bone for the lower arm, one bone for the hand (we'll probably need to reshape the fingers to be holding the gun), etc. The more bones there are, the slower the transformations will be, obviously. The exact layout doesn't really matter so long as it looks right.
One thing I will need, though, is a bone to specify where the gun should be attached. I'll probably just use the one on the hand, but I might need a special one that's offset a little or something.
