I initially was unsure about the CR mechanic, but once I'd played a while and saw how logistics, CR and cargo capacity tied into each other, I became a big fan. CR can be tied into a lot of new game mechanics, and I like having to make choices about how to deploy my fleets. The supply mechanics give me a whole new appreciation of the Hound, which has great capacity for its size and is fast enough to chase down retreating enemies. I am trying out fleet combinations I never would have bothered with before, and it has opened up the game for me. CR is the restriction that allows you to define yourself within the game, and is an excellent core mechanic. It might need tweaking, but I hope it is here to stay.
As an aside, the CR reduction for participating in combat may seem extreme, but keep in mind that the ship is straining its systems to travel as quickly as possible, shoot quickly, and maintain energy fields. The universe of starsector is one where a great deal of knowledge has been lost and even experienced crew don't necessarily understand how their equipment does what it does. Complex equipment cannot be run ragged over and over again and maintain effectiveness. I found my new logistical vulnerabilities fun and satisfying. And while the AI does not have the same supply concerns, their CR concerns mean that you can harry them to death, and really be a raider, which is great!