The reason is weight and balance. The CR2 is nose-heavy and we need to put as much weight in the back as possible. The SkyWest CR2s are very nose heavy due to a design change in the rear of the plane.
None of the CRJ's have missing windows -- unless they are so scratched by years of abuse where it's worthless (ExpressJet I'm looking at you and your decrepit CR2-AS/CR7-QX birds). If you're looking at a 9 and see blocked windows in the front, it's just the galley blocking them. The CR9-NextGen's have large windows high up where you don't have to crunch down to look out of them.
I'll fly on a 200, but it's not by choice. I'd rather have a E145 or a 900-NG. Sadly, CHQ is the only operator in the DL system with EMB135/145s.
I'd have to speculate W&B is also why the gate-blocked row is row 6 instead of the last rows in the aircraft like every other plane in the system.