You need it to upgrade research-improvements and for the movement-support modules,

so early game its really not worth all that much

So... I'm guessing none of you have made commanders...

The flagship gets you extra stats, of particular value early on is the doubled speed, but it's a defense/offense free ship, the promotions are all promethion, and get you ships with better stats, different boosts, etc.  They're also all 0 logistics.  With 3 citizens and 20 promethion you can make a super fast, super buff fleet with unholy badass levels of awesomeness in the early game when the AI is running around with 1 attack ships.

If you have loads of the stuff, you can even afford to shuffle a bunch of workers from planet to planet, getting your production powerhouses off the ground faster and then transferring them back out to put them somewhere more useful than the ship facility that builds it's improvement upgrades in 2 turns.

pretty much every citizen type that has promotions are mainly going to cost Promethion first (10-20), then some other very minor volume of something else (and/or ideology).

So it has early game uses if you get some of the other stuff.