The RTR version was basically an attempt by Roundhouse to have the kits assembled in China. Very few modifications were made. An improved motor was installed, but I don't know of any other major changes.
Because of this, the Chinese assemblers ran into the same problems kit builders did. Problems with gear flash, and timing of the closed loop between the center drive shafts and gearing and the line shafts and gearing are not unusual. The Roundhouse-supplied electrical pickups are not the best, either.
Many RTR Roundhouse Shays strip or crack their plastic gears when the mechanism binds from the gear flash or timing. Some RTR Shays incorporated the "fixes" kit builders learned about (opening the lineshaft gear loop), and run quite well. It's really luck of the draw - but I'm guessing the later the Shay was assembled, the better the chance of it running well because of experience gained on the part of the assemblers.
As has been proven by Roundhouse, Bachmann, Bowser, and other manufacturers, a kit is not the best base from which to make an RTR locomotive. Bachmann designs their locomotives to be assembled in a factory, and doesn't make kits. Those who have tried to mass assemble their kits have generally run into difficulty. The kit builder has time to check and perfect the fit of parts; the factory assembler doesn't.
Personally, I would choose the kit because I can take the time to make it right (I have an MDC Shay kit in the queue now). At the very least, demand to see the RTR model run before purchasing (or adjust the price for the risk). Unstarted kits have gone for as low as $45 this summer on eBay.
my thoughts, your choices