I find it funny that people don't seem to realize that the game is currently in a very transitionary phase. The last version was fine because there weren't a lot of loose ends to worry about. Everything worked well enough together, and the game delivered a fairly unified experience.
Problem is, that experience from the old 0.5 versions in no way represents what the final version of the game will be. With the campaign starting to take shape, Alex can't really develop in modules anymore. There comes a point where you have to start adding in features that will more or less appear in the final game, and because, obviously, 0.6a isn't a feature-complete Starsector, there are going to be some pretty big holes in those features.
Boarding is probably the best example. I find it hilarious that people don't realize that the new version of boarding isn't really designed to acquire new ships--it's meant to acquire new blueprints in the future (At least, this is what I recall Alex saying a while back), which is something that hasn't been implemented yet.
So really, instead of everyone going "baaaaww CR ruined the game" or "baaaaawww boarding ruined the game", people just need to chill out and wait for the game to near completion. If Alex made the 0.5a versions as fun as they were, I'm 100% confident that version 1.0 will be infinitely more fun.