From reading around the forums, the transmission issue sounds like the only really serious reliability issue that a significant number of people have reported. If you are hearing any kind of unusual sound from the transmission, I would definitely get it looked at while you are still under the powertrain warranty. And they probably won't be able to figure out what the issue is without tearing it down, so don't be afraid to push for a new tranny if it sounds like something is really wrong.
Other than that, it sounds like some of the seals may be prone to leakage, so watch for fluids under the car. Also, some people have noted the paint is really soft, which I can attest to. My FiST came with dealer installed swirls and my hood looks like swiss cheese after only a month on the road.