Last year most of my flying was domestic mid- and trans-cons, primarily through ORD and IAD, flying Skywest on the western end and the 'others' on the eastern end. Shockingly, I had more issues with Skywest than with even Mesa and, gasp, Colgan. Skywest, amongst more mundane issues (handling irrops, etc), presented me with no less than four failed aircraft, one of which failed on takeoff, that after sitting around for three hours after the previous aircraft failed at the gate. I ended up in a SuperShuttle on a two hour cruise to my destination that night.

All year, I kept expecting the worst from Colgan, Mesa, et al and they failed me miserably by leaving on time with functioning planes. Who'd have thunk

OP, I'll qualify that I do fly a lot of 'puddle jumpers' where you're talking about RJ's so your experiences will likely differ. I've had few issues, save for weather-related, on any regional jet, by any carrier. I'd say go with what fits your needs the best. I recall, flying into ORD on RJ's, that sometimes we end up at the E-F gates and sometimes at the C concourse. Same at IAD, wrt A concourse versus the mainline gates. If you fly a regional carrier, it's a crapshoot.