After 7 years and over 5000 hours on the CRJ200, the 2 biggest problems are the flap runners and the apu door actuator.
If you operate them in a cold WX environment where you need to deice, you'll find the apu will develop a high pitch whine if the deice crews inadvertantly spray fluid in the apu inlet. The whine is the bearings, which will eventually give out.
Pax prefer the EMB's but I found the CRJ to be an easy plane to operate and extremely forgiving for low experience crews.