Limitations
Acceptance
Like many of the upcoming sustainable systems that can be added to homes, the acceptance by the general public is usually low. Many people don't consider geothermal systems to be an option, but it is a great one. Similar to solar panels, wind turbines, ect., geothermal systems are being ignored by many. As time passes, though, acceptance grows. Hopefully one day geothermal systems will become one of the most popular HVAC systems so that we can take more advantage of our renewable resources.
Cost
During construction, the costs of geothermal systems can be very large. The installation of these systems ca be complicated and not all contractors are capable of working with it. This means you would have to find a contractor with enough knowledge and skills to complete the job, which could be more costly. In many examples today though, there are tax incentives to help decrease the original price of the system. The initial costs may be high, but in time you will be saving a ton of money in energy savings.
Land
These systems can require a lot of square footage to be installed. Horizontal underground wells require much more area than vertical wells. If you are in a location where you don't have a lot of square footage, you may not be able to install a geothermal system.
Refrigerant
If refrigerant is used as the fluid in the underground wells, there could be a few issues. Although it would work really well to transfer heat energy, if the pipes burst at any point there could be a huge problem. If the pipes burst, the refrigerant would be let into the ground, causing groundwater contamination.