I do not think removal of flux cost is a big deal, not enough to weaken Wolf or Medusa. It is not often that flux cost stopped me from skimming. Three charges is the primary limit that prevents skim abuse. Now if skimming became unlimited, then there could be a problem.
Medusa is really good as a flagship, but for AI, I do not think Medusa is much better than an Enforcer. I prefer to use Enforcer for AI because they and their weapons are more common and cheaper to deploy. If Medusa gets weakened, I want deployment and supplies costs lowered to match other destroyers. Being limited to 600 range with most of the best configurations kind of hurts.
As for Wolf, it is not that great a frigate. I do not use any for endgame. It is not as cheap as a Lasher, and it is not as fast and powerful as Afflictor, Tempest, and Hyperion. It is good early in the game, but its weaknesses hurt it later.