I have to respectfully disagree about the complexity of the geo system. As a forcd-air system, it is really no different than a typical heat pump. It just exchanges heat in water instead of air, a much more efficient process.
One benefit of a geo system, as mentioned before, is it uses its waste heat to heat water. I do this process in a standard 80 gallon electric water heater, with the breaker turned off. This tank feeds another 80 gallon tank that takes over if needed, but at least it always receives water significantly warmer than it would directly from the well.
Now if you have radiant heat in your floor, especially in a concrete slab, you do need some fancier controls because of the thermal mass. This is a whole different topic.
Assuming geo with floor heating and AC.
Since each room has at least one but usually several floor loops it is easy to control temperature in every room (zone) separatelly. As opposed to natural gas, oil or propane furnace the heat pump can heat HW cheaper than direct heat. In fact it will heat HW for free by waste heat when AC is running. All this require temperature control for each loop.
So typical three bedroom house will have:
1.) Eight zones (kitchen, living room, bedrooms 1,2 and 3, garage, bathroom 1 and 2.
2.) AC temperature control (one for whole house or also zoned).
The zone thermostats for floor heating use different temperature algorithm than thermostats for forced air. The issue is a lag time between introducing the heat in the room and the temperature response. For forced air it is measured in minutes. For floor heating it is measured in hours. The thermostats are actually simpler because they are not programmable.
3.) HW temperature control with a logic that would enable direct heat when heat pump is not available.
4.) Heating/cooling accumulator with two heat and cool temperature control loops. The control loops control the temperature in the same vessel but have their respective sensors on different outlets.
5.) Logic switching between heating/cooling mode.
6.) Recirculation pump "excersise" function to spin all pumps for short time every day to prevent stiction. That is especially important for variable speed pumps set to low speed because they might not start after one season of inactivity.
I see the difference in the fact that for furnace forced air all the controls are more or less standard and built in the system. Just add a thermostat and you are ready to go. Geothermal with floor heating is designed according to specifics of particular house. I believe that purposely made programmable system for such application are already on the market making application of the geo and its efficient use easier.
When I built my house I was quite naive and thought that the guys installing it will install all the necessary equipment and proper controls. Only later on I learned that it wasn't necessarily the case. They made it work reasonably well and it was about it. So I built my own system. It was fun project but after the experience I would buy off the shelf controller and use it. Therefore I would strongly advise to avoid custom made systems based on a PLC and similar for most homeowners. The issue is maintenance and repair when something goes wrong. Most homeowners will be better off with off the shelf product that can be troubleshot by average HWAC tech. I built my own control system so I can fix but I doubt that average heat pump or HWAC tech could come to my house and deal with possible problems. Heck I have problems to fix program bugs etc sometimes.
Integrated of the shelf control systems are available from
http://www.tekmarcontrols.com/literature/a.html 
