They switched to FMod because of all the features it introduces that you just couldn't have without complex programming.
If you remember the doppler shift of audio in the old system never worked right. Fly head on past my Lanc, B-17, or B24, or HTC's 262 to see what I mean. Plus, FMod allows sound files other than .wav format. The .ogg format is much smaller, so the final bank files are smaller too. Also, the FMod editor includes all the mixing features you need.
I would bet the overall processing of the .bank files for the game is much less than .wav files, which means a game that runs better.
FMod can do more than AH3 needs, which allows for more expansion and game growth.