I would choose a 2005-2007 model CR as a starting point, the last incarnation of the CR model. This bike has many strong points; light weight, it's an excellent neutral handler, has good suspension, and is just a blast to ride. My 2006 is bone stock engine wise with the exception of an FMF fatty and silencer, v-force reed and a JD jet kit and I like these mods.
I am in the process of a build on this 2006 CR250R for moto and have done a lot of research on what other folks have done with the engine setup (the common complaint with late model CR's was the lack of bottom end snap and inability to properly jet the stock Mikuni). I have come to the conclusion that the best mod is to replace the stock mikuni with a keihin PKW airstryker 38 and this will be my next purchase. I'm starting to regret the money I've already spent on the mikuni at this point. When I rebuild the engine I'm also going to have some cylinder/head work done and bump the compression a bit. This is probably all I'm going to get done and with the other mods should be all the engine I will need.