I also see option 2 as the best compromise. There will be problems with small weapons, like pistols or knives since they will be barely visible on certain outfits but still better than not having them be visible at all.
As for the body changes, I didn't think about them that much yet. Someone wanted me to add more height stages, which would be close to impossible with current system. But if I manage to lower the number of weapon sprites to do this, I might as well do a little extra and add weight and stuff like that. I might even be able to allow people to play as a guy (Wanted to do that in the early stages before the sprites bloated everything) and together with mutations and cybernetics, the amount of things I could do is really large. I might also not do any of that and focus on giving main character more poses and expressions in dialogue. Looks like I have a lot to think about.