For me the big things are ditching Push The Limit and Veteran Instincts. I think this creates a great deal more control over what a ship can combo together and how powerful that is. Something that is fair moving early becoming unfair when moving later can be prevented because you can't change when it happens via pushing up the Pilot Skill.
The Push The Limit change does that as well. Ships won't have a blanket extra action allowing dialing in the perfect order for ships to do things. Ships won't be able to put two things together that shouldn't be allowed together.
Those should be terrific balancing mechanisms all on their own. And more to the points about "fun" they should serve quite well in preventing things that just flat out "feel" unfair and thus become unbalanced.
Edited by Frimmel