disclaimer: I only got to page 9 before tl:dr-ing this thread, so it's possible that my opinion has already been stated.
I like Combat Readiness. I grew up watching Star Trek, and the CR system seems to hold true to the space battles I used to watch on the telly. How I see it is, at the start of the battle at full CR, the red alert sounds and all hands are on deck. Then during the battle, the ship is taking hits.
Now how Star Trek did it, even if it was only the shields that were hit, you'd have computer panels exploding throwing redshirts here, there and everywhere. This is what I imagine is happening when CR decreases.
As to why ships can't do battles in a row, think about it. You've just come out of a battle, and you've got broken panels and wounded redshirts all over the bridge. You've got to spend some time fixing them (chewing through your supplies), and getting some hyposprays into your redshirts. This takes time, hence the long CR recharge.
Just because your post-battle stats say you didn't lose any guys, doesn't mean they aren't wounded. Likewise, your hull may not be damaged, but exploded panels aren't part of the hull.
And this is why I like CR. It makes me think of the space combats as more 'real'. Consequences, and such-like.