In my opinion, Makerbots are great for beginners who want to learn about the printing process as quickly as possible. They require minimal tuning out of the box in order to create great prints. They're great plug and play devices. On the the other hand owning a RepRap requires a significantly higher knowledge technical skills in order to calibrate the printers. RepRaps can take longer to start making good prints, but the knowledge you gain about the printing process and how the printers operate is invaluable. It's kind of like Mac vs. PC. The only thing that matters is how involved you want to get with understanding the machine.