Thanks for the notes :) I had the opportunity to play CL at a party this weekend, and it was the first time in years that I've really sat down with it. I agree with a lot of your points — its difficulty running even a moderately complicated creature smoothing is a major issue. I did as much rendering optimization as I could back when I was developing it... unfortunately I think it's at the limits of its technology; the physics sim is the biggest bottleneck iirc.
Axons take up tiles because 1) they need to be selectable so you can inspect them (important for a lot of classroom applications) and 2) action potentials used to have to travel down the length of them and they were all different electrical compartments. The latter was removed to make creatures more responsive, but the engine still relies on them being that sort of entity.
Crescent Loom 2 is still a number of years off (gotta finish LT), but yeah more robust combat/opportunities for creature interaction and a map editor are going to be very high priorities for it. I really can't wait to get back to this. There's so many rough edges that a better underlying engine would solve.