I am doubtful that Disney would do something to reduce the wait times for FOP. I hope they do adjust it, but I won't hold my breath.
1. They have to staff it, which costs money. It saves money to run only one theater.
2. Disney uses wait times for crowd control and they want people to spend time in other areas as of the park also. FOP is arguably the most popular ride in AK and WDW as a whole. People would spend all night riding it if they could. After experiencing a 30 - 45 minute wait people would move on to other rides so they aren't wasting time standing in line for FOP all night.
3. Higher wait times supports the idea that FOP is the best ride on property. Getting to ride it once is special; getting to ride it 2 or 3 times is like finding a golden unicorn. A lot of people would be satisfied with one or two rides.
From a quick search I found the ride capacity per hour as 1,440 people. Anyone know how many tickets they sell on an average DAH night?