It almost looks like the bone in Serge's left upper arm is curved there, although I suppose it could be just an artifact of the screenshot. I wonder--are the shoulders truly, conceptually translating, or did they just use that as a kind of shorthand for rotating the upper torso, shoulders included? I don't know how you re-rigged this, but if you followed the original pattern, the shoulders aren't connected to the spine at shoulder level, as would be expected based on the way a real human skeleton works... (I may be too hung up on how real human skeletons work. If so, I apologize.)
About the number of joints--I think that line refers only to the overworld models, but it's possible that the reason for some of them not having weapon joints may be due to something other than a joint number restriction (in fact, from the look of it, all of the overworld models should have a couple of unused joint slots, since the max listed is 30, for Leena and Riddel). Maybe those characters just never participate in a sequence where they pull their weapon before a combat has actually started?