I have both. I built the cnc router last year and just finished up a bootstrap mendal this summer. I used the router to build the mendal. In my experiance the cnc router was very easy if you go with all the popular components. Mach3 has been amazingly reliable compared to what it avaiable for the reprap. G540 is rock solid, etc..
The challenge with the reprap was the extruder. I believe that a number of companies are trying to sell this stuff. They give you an idea how it works (because its all open source) but I found that these extruder designs don't work. I think they hope that you get frustrated and buy their product.
The software needed to reliabily drive the hardware was the next big problem. I eventually got ReplicatorG to work. Be ready to do a lot of searching to find key tips on free open source software.
I won't recommend trying to use the software/hardware currently on the market (except EMC2) that is designed for a 3D printer on a CNC router of any size. It extrudes at 31mm/sec which the router is capiable of but the controller is very crude compared to Mach. Jerks the steppers around is best I can descrbe and I really don't trust it to drive a gantry machine safely. Again EMC2 might drive both machine but I'm not a Linux fan.