When I went to Bhutan, I did the Taj in Thimphu, Zhiwa Ling in Paro, and Amankora in Gangtey. You could certainly do Amankoras all the way. The one in Gangtey was absolutely amazing, and I heard they are all essentially the same.
The Taj was pretty good, and I really liked Zhiwa Ling. If price is a significant factor, then certainly mix things up. I didn't feel all that let down by mixing in different hotels, although obviously the Amankora is a big step above anything else in terms of service.