Short answer: Yes - Upgrade time/Reserve time/Pay (kinda)

Long answer:

Obviously there are less ERJ bases than CRJ bases. If you want the west coast soon then go ERJ, if you want midwest soon (ORD, DTW, MSP) do the CRJ.

Upgrade times and reserve times are lower for the CRJ, but it depends which base. For example fastest upgrade overall is CRJ DTW, but a junior ERJ base could upgrade sooner than a senior CRJ base. Same with reserve. Overall, CRJ has less reserve time (DTW) but a junior ERJ base could have less reserve time than a senior CRJ base. Currently they have a 2 year seat lock, but I know guys who did FO on the ERJ and are upgrading into a CRJ.

SkyWest's website has the official list of junior CAs and FOs by aircraft and base here: Pilot » SkyWest Airlines

(Just scroll down to the "domicile map/seniority" tab)

Pick your poison. Both aircraft seem to have some pros and cons.