For the builds I've been using, I don't find the fleet upgrades all that interesting/exciting/useful. The Command Variant has a strong squadron value, but so does the AFA2B, which is more expensive but faster, harder hitting and more survivable. I had thought the Pelta assault might be able to pull off the Flechette/OrdExperts/Black Dice combo, but it crucially lacks the weapon teams slot.
So...help me out here. I expect the answer is going to be primarily: Fleet Commands and no other reason. And also you don't like fleet commands and are thus, in fact, a dullard of the highest calibur...but even if that's the case I welcome insight outside my own.