The fix to the scaling issue is a pretty heavy nerf, we'll see how that settles out.
I started a new game to test the new enclaves/NCCs in isolation, and they're about in line with normal starships now (less damage, but greater range, and provide some survivability boosts). With effort (and both enclaves/NCCs up to mkIII), I can clear out a planet with no casualties, but I could do that with twelve mark-caps of most starships. So, mission accomplished.
Also, a couple things are really annoying, and think fixing them might be really easy:
TINY threatfleets will make a relay. Killing every stray AI ship is tedious, and will often release more, and even if you scour the planet, it can always reinforce right as you leave.
Minor faction patrols go onto enemy planets and die. That's fine for a zombie network, but resistance fighters/dyson gatlings/freed nebula allies should defend only, even if they don't have the awesome high-level enclave logic.