I haven't riden a CR or an RM, but i can tell you this, if that RM is $2000 less i would go for it. Even if there is some reliabiliy issue, wich i doubt there really is, just think of what you can do with all that money you save. You get get a new helmet, revalve the suspension, get the motor ported, buy a nice set of bars and still have money left over.
In the end, the RM will be faster, and the suspension will be tailored to you. I have a 2000 KX250 and people say that they arent reliable either, but i haven't had any major problems with it at all. If you take care of it, the bike will be fine.