The problem many have with Eagle is the one year seat lock, geographicly dispersed fleet types, and far-flung domiciles. Since the ATR is only based in SJU and MIA, the Saab only based in LAX and DFW, and the CRJ only in ORD and DFW, being committed to one of those fleets and thus regions is scary. XJT in comparison has only one fleet type, so if you get IAH or EWR and want the other, you can reasonably expect to get there in short order. Likewise, if you apply to Air Whisky you know you will be based in the Northeast; Comair you go to CVG, ASA to ATL, PSA to CLT. If you can't live in, or commute to one of those cities you just don;t apply to those carriers.
While Mesa and Skywest approach Eagles' geographic dispersal, the ability to change domiciles is much easier.
And SJU is a deal breaker for so many pilots.

I'm now on day three of Basic Indoc. 16 in my class, 8 ERJs(4 LGA, 4 ORD) 3 SF3s(LAX) 5 ATRs (2 MIA, 3 SJU). Had I not been able to hold the ERJ I would have quit on the spot. Not everyone is in a position to take that chance.