As far as Eagle goes, you aren't exactly comparing them to the highest paid airline out there(note also that their guarantee is lower than Chautauqua). Also, upgrade time over there is supposed to be one of the longest out there. Not that I know from personal experience, since they're not my airline, but we've got a bunch of ex-Eagle guys working for us. Talking to the FO's I've flown with, the lack of a decent upgrade time is the biggest frustration. That and lousy relations with management, backed up by lousy relations with the APA.
Of course, since I've never flown there, I could be all wrong, but that's my perception of them from the outside.