The biggest problem I have with the CRJ layout specifically, and this a right seat problem.... I'm constantly reaching across for the FMS, and god forbid the capt is hand flying, hands on thrust, when I'm trying to put something in the FMS..... I'd much rather have the FMS where the RTU is, because I can do just about everything the RTU can do with the FMS, but I can't do everything the FMS can do with the RTU. Also the EMB145 (still speaking FO here) has a PTT on the upper right side so you can answer a radio call with your right hand and change the ALT, HDG, etc with your left. Yes it can be done in the CRJ but you have to use the one on the yoke and a lot of people don't like you touching that if they're hand flying at the time. Plus I don't really like the 'pull down' type switch they have installed. The other layout problem i've heard about, but thankfully never had to deal with. The manual gear extension is supposedly hard to get leverage on. I've heard stories of folks having to stand in the flight deck to get enough strength to pull it. Never tried it myself in the plane though. (knocks on wood)