All the makerbot does is find the lowest acceptable bar for accuracy and repeatability...which is pretty damn low when comared to even hobby CNC XYZ systems. They can get away with it because the maximum precision the can get from the medium is relatively low as well. At the end of the day the only think that makerbot has going for it is that it is an additive process instead of subtractive.
The real devil with all 3D printing (additive CNC) is that it is, at its core, a materials science problem. You can throw better software and hardware at the problem until the cows come home. Until you solve the fundemental material science problems you will always be better off with a 5 axis mill if you want to build stuff that is actually usefull.