You're right, PuzzleScript isn't a universal puzzle game-making tool. It's best for turn-based, keyboard-controlled games where you're moving a thing, or several things around. It would be neat to mod it to allow for mouse-controlled games - I'm a giant fan of qrostar's games.
I'm a bit burned out on this right now. I've been working on the engine for a couple of weeks, energy levels, and in order to reenergize I need to see people make good use of what's in there. Adding mouse-controller support wouldn't be that hard, actually, but I'll need some encouragement.
Ditto the above to realtime stuff, animations/smooth movement between frames, what have you. All very reasonable possibilities. I just have to see where things go.