Sensor Battery Life: The big drawback is that once your sensor's battery dies, you need to buy a new one. I hear that the average lifespan is approximately 1000 runs, which is not all that bad. If you like the system enough to get that much use out of it, you likely won't mind dishing out for a new sensor either.
Finalizing Workout Data Could be Easier: At the end of your run you need to press the Menu button and then scroll the clickwheel down to the End Workout option. This can be tough if you are bent over and huffing and puffing in exhaustion, with little to no control over your fingers! (Maybe I need more conditioning!) But seriously, there is nothing as frustrating as pushing yourself on a long run, only to lose your data by accidentally clicking the wrong button upon your return. I think Menu, then hold center button would be a better way to end your workout.