This will cause a stir with some, but I moved HVAC out of the home automation system and have been very happy with that. In our previous home I ran a serial stat through the Elk (been over six years, so can't remember which) after using a X10 model prior to that. They worked well enough, but all they really did was allow for scheduling via the Elk and setting the system into an "away" mode when we were leaving and arming the house, which was no major advantage. I just kept the existing programmable stat when we bought this house and I installed the new Elk and ISY here about five - six years ago (left old ones in other home).
When the stat here had an issue (power surge may have affected it) and Nest was coming out with their 2nd gen device, I figured I'd give it a try. Very happy with it! What I found was that while I had a second app on my phone, I didn't much mind that. And with a geothermal unit, you will likely not vary your temperature much throughout the day, so putting the system in "away" mode will probably only be used for vacations.
Now, this does bring up the whole cloud vs local control, Big Brother / Skynet debate... I maintain that this is WAY overblown. If the Nest (or similar) can't reach the internet, it just functions as a normal, programmable stat and runs its program. And I have found their system very reliable for maybe three years now, with it being unreachable only rarely, and even then back up within minutes. In fact, I've had more issues with the M1XEP than Nest, if that says anything. The only real drawback is that neither the Elk nor the ISY can speak directly to the Nest, which made it harder for me to use one when I decided to hack a pellet stove recently (hardly a normal situation, and I solved it by using Homeseer, which finally gave me a reason to make use of that largely unused license / software).
So, don't think you have to find a thermostat that uses the Elk or ISY. It's a nice to have, but you can get automation, convenience and great control without doing so.