Here's the short of it:
The MakerBot is "out of the box" ready. Plug it is and start printing. The down side it that you really can't upgrade it.

The RepRaps are typically built by the owner, so you learn a lot about the technology, while you are building it. You can modify it, print replacement parts for it, and even make a whole new config, if you get creative.

It's kind of a "who are you?" situation. (as BurnIt explained it)