The drive to Bumthang is indeed long and rough, so if you can fly there, that would definitely add to my preference for Bumthang over Thimpu. Bumthang is by far the least touristed of the Aman locations in Bhutan, and the Aman lodge is wonderfully located right alongside an active monastery, so your fly-on-the-wall view of the proceedings there is really unique.

But I wouldn't sweat these decisions too much -- Aman will provide you with special experiences regardless of which lodges you choose, and the other poster makes a good point that if you want to experience "urban" Bhutan with lots of shops for tourists, and to go to bars and interact with locals that way, perhaps Thimpu will be memorable.

The temples are very similar across the various valleys where Aman lodges are located -- and the access to local ceremonies is something that Aman will cultivate for you. So while Bumthang was very special for us because we met the king there and interacted with him and his sisters the crown princesses, and attended a fire ceremony late one night in which the villagers ran through a tunnel of fire, a wonderful thing about an Aman journey through Bhutan is that you never know which stop will have such experiences, and Aman will do their best to find them for you, so again, I wouldn't worry too much about one lodge over the other. The drives, while grueling, were the most spectacularly beautiful I have ever experienced, particularly the stretch past Punakha and up to the high altitude of Gangtey, with hanging rice terraces, prayer flags atop the hills and peaks, yaks, and tropical plants and evergreens, such is the diversity of the terrain and climate.

So while I strongly preferred Bumthang to Thimpu, if Bumthang presents challenges to the travel times, I would trust Aman and go with Thimpu over Bumthang.