Interesting thoughts, guys. Thanks for the posts.
My thinking was also that to avoid a rebalance (which may not be an issue, considering that's a part of what's going on during the beta testing phase), you could have just a few levels:
green/rookie crew: effectivly 85% of current standard damage/armor
veteran crew: effectively 100% of current standard damage/armor
elite crew: effectively 115% of current standard damage/armor
I wouldn't want starbase experience to be dependent upon combat because they don't move, and as such your oldest bases may never gain any until it's too late for them.
As for adding additional slots, I could see that as being a potentially easier way to go except it seems too much like they'd be viewed as static capital ships. I'm not sure if that's a valid concern either, but I figured I'd put it out there as well.
Go ahead and rip my ideas to shreds at your leisure 