I wouldn't give up a Flight of Passage FastPass for a Na'vi River Journey FastPass. After you ride FOP, there's a good chance you're going to want to do it again.
A few observations:
The NRJ queue is not as entertaining as the FOP queue. A very long part of the wait is in a very large room with many switchbacks. It's nicely decorated, but frankly gets boring after a while. When I did this attraction standby, it was about 40 minutes in the evening and it felt really long. I didn't like the ride that much, so for me the 40 minute wait wasn't worth it.
The FOP queue, on the other hand, is one of the most spectacular I've ever seen at a Disney park. There are many different rooms and each of them is beautifully decorated. It's worth going through the standby queue at least once (although I wouldn't give up a FP to do so... maybe if you choose to ride it again standby). I walked through this queue at an 80 minute wait and it felt long but entertaining.