Man, tough call. I've really liked it here at Skywest, but I have a friend who's been at Expressjet for a while and he's enjoyed his time there. I would go with bases. At Skywest, our junior bases are ORD and MKE in the RJ. Although after a few months to a year, you could probably hold whatever base you want. Upgrades are running about a 1.5 years on the RJ and 9 months on the Brasilia (if you've got the time, of course). I'm pretty sure the junior domicile for Expressjet right now is ONT. If the branded flying works out in California, it would be cool to be in on the "ground floor" of that operation.
Skywest is 65 hours of pay at the new hire rate of 19 bucks/hour. Pretty bad, but at least it's something. Changes to 75 hours once you're done with training and on reserve. Double occupancy on the hotel room, but I wouldn't let that sway you one way or the other. Yes, it sucks, but it's the first two months of what might be a long career at Skywest. The first year pay is much more important, in my opinion. Hope this helps and good luck with your decision.
