The main disadvantage is that you (usually) have to pay for it! Air is free. Also, you have to keep filling it with nitrogen (not air) to keep the benefits.
There are lots of advantages, but on the disadvantage side, its quite expensive to fill your tires with Nitrogen. Also, not many places may have nitrogen filling capabilities. That translates to higher maintenance costs.
Scientifically there are zero disadvantages! None. If you fill at tire store and pay once, they will refill for free. It will save on average, 10% when looking at everything involved. That is far more that what it costs. ($600 x 10% = $60)