Okay, I just got back from WDW, here's my take: If you're concerned about skipping Flight of Passage based on what you read here, I recommend that you reconsider. (If you're going to skip something, skip Na'vi River Journey... ugh what a boring ride. Not worth my 20 minute wait. But I digress. Forgive me, unlike most people, I hated the movie Avatar.)
This is no way intended to take away from the OP's valid experience and frustration. OP gets to have their gripe, but some of the posts on here are piling on out of control. I get it... reading these forums can make you even more jaded and think that the company is doing everything wrong, constantly. Instead, I was glad to discover that the majority of guest visits--including my own--have been trouble free, and many people are opting to go back and ride more than once even without a FP+. When speaking with my own group, when overhearing guests elsewhere, and when complete strangers chatted me up, the talk is about how the ride is amazing and in some cases, how it is "totally worth it" to get back in line for another 160 minute wait. You read the comments here and you'd think that all the CMs have become rude and the ride is a disaster.
My experience was the opposite. We rode the first time with a FP+. Then decided to go back again at the end of the night, an hour before closing when the queue said 160 minutes but the wait was more like 90. The attraction is amazing, and even the queue is amazing. It made us giddy and it ended the trip on such a high note. The fact is this ride is making many many people very happy with their visit.
All four theaters are usually operating quite well for a new attraction, and they are fully independent. Of course, a fire alarm is a different matter. If you look at the sheer capacity of the building, you'll realize why a quick and safe evacuation is the priority in a fire alarm.
Ultimately, I walked out of Pandora -- initially thinking that it was a desperate move to grab some IP to compete with Harry Potter -- to really thinking that Disney still keeps upping the bar for itself and its competitors. Game on.