I have to say, running an OS drive over USB may not be so bad. For my quite old Mac laptop, I have an old image of my OS X installation (10.6), and a clean installation of OS X (10.9) installed to an older LaCie/Seagate 2 TB USB 2.0 drive. While it's not a speed demon, I find it to be quite usable.
But since you have the dedicated space for an internal drive, I can see how that would be preferred. :iagree: