Republic would be the safe bet. They do what they do and they do it pretty well. Pay and benefits aren't the best. Definitely not the worst either. The are growing modestly (mainly just shifting airplanes around, but I think taking delivery of 170/190s still) and have bases all over.
The next 2 to 3 years will either be very good or very bad here at ExpressJet. The charter thing is doing well and there is a lot of money coming in from there in addition to our CBAs with Delta and Continental. That said, the ExpressJet Airlines thing is a big question mark. The general consensus around here though is that if any management can pull this off, ours can. Upgrades are running consistently 24-30 months and there is a lot of upward movement. Most guys are off reserve in less than 6 months (faster in Houston, a little slower in Newark, impossible in Cleveland). If the branded flying takes off and we start getting new airplanes, it would be a very good time to be here at Express. If the branded thing tanks and Continental pulls more flying from us then there might be better places to be.
Bottom line: its all a crap shoot. Especially chasing an upgrade. If theres an airline that has a base where you live or want to live, go there. Commuting is miserable and will significantly impact your QOL. More than a few guys have prolonged their life in the regional world by jumping from airline to airline chasing an upgrade. No matter where you go, what is true today will not be true in a year or 2 when you are eligible for an upgrade.