I flew for CommutAir several years ago, so this information is a little old, but I've heard not a whole lot has changed since I left, so hopefully it will be of some use to you...
The pilots at CommutAir are awesome. It's a tight-knit work group that interacts more like a family than a group of employees. They are top notch aviators and a lot of fun to work with. I learned more about flying at CommutAir on the B1900 than I had in all of my flight training. New hires at other companies that go straight into jets have a tendency to knock the turboprops, but the majority of ex-turboprop drivers will tell you it was the most fun they've had in their careers. In my opinion, you'll be flying jets for the next 30-some-odd years... You'll never have another opportunity to fly a turboprop. Get it in while you can - I'm glad I did.
The relationship that management has with the pilots is remarkably good. They are non-union (voted down ALPA a few years ago), simply because the pilots there do not feel like they need protection from a management group that takes such good care of them. (Every company has its issues, but their management team is not "out to get" them.)
When I worked there (you should try to verify this info, as it's a few years old)... The company paid for 100% of our medical insurance, and everyone was guaranteed 13 days off a month. You bid for pairings on your choice of days - not hard lines or PBS (so you could buddy-bid with your friends, and if you were senior enough, get your choice of days off). They spread reserve out amongst the pilots so you didn't sit any more than 1 week of reserve each month. And I don't think you were allowed to be assigned more than 1 week of stand-ups in a month. I thoroughly enjoyed it there, and would go back and do it again in a heartbeat. Truly, some of my fondest memories of my career come from CommutAir.
I can't comment on Mesaba. I know they had some issues a few years ago in the whole whip-sawing movement between them and Pinnacle. I will say that with the CRJ-900 on property, if you wait it out there long enough for an upgrade, you'll be able to get PIC Jet (versus PIC turboprop) which you won't get at CommutAir.
My best advice, if I were in your shoes... I would be asking:
1. What's the current and projected upgrade time on each of the aircraft at each company?
2. What's the future viability of each company? (Will Mesaba be affected by a DAL/NWA merger, or when does CommutAir's contract with CAL expire, for instance.)
3. Are either of the companies projecting growth or shrinking?
4. What is management's relationship with their respective pilot group?
Good luck to you. I hope this helped.