They both significantly improve squadron use.
Either can be used on The Victory-SD or the Assault Frigate.
So which one is the better choice...?
Whichever is better suited to the situation you find yourself in. Neither is flat out better than the other.
Flight Controllers does nothing to help your bombers on their attack run. Expanded Hangars isn't as cost effective on your fighters trying to take down enemy squadrons. (you still need to pay for the extra squadron to get a similar number of extra dice).
So .. why not both ;-)