The idea for proficiencies is that they will be a character's ability to use the tools available to them.. and so there would be different proficiencies for different tools. (So, you could pick up Proficiency: Bow (crossbow), or Pistol (pulse gun), or Chisel, or Hammer (rock). Then skills would be different things you could do with those items, or without. So skills might include Tumble (ability to take a fall), Repeating Shot (fast action with a projectile weapon), or Small Figure Carving (which could go with the Rock Hammer or the Chisel proficiencies, potentially).
Hm, y'know.. have been having trouble sorting these out in my head, and typing seems to have fixed that. Could probably still use some advice, but.. at least things are coming to mind now. The major thing is figuring out how to incorporate them into the system; how they will effect outcomes, what kind of success percentage a character would have. Suppose that'll all come in due time..
Oh, and for anyone wondering about the Transformers game thing.. that's not entirely dead. Just put to the side while this project (which is based on ideas from much earlier) progresses, and may well end up being an adaptation of this system.