focus on power production and make fuckloads of interdicting defense platforms if they're small enough fleets (which, knowing federations, they damn well will be)
Also, fuck federations fleets. I made a 300 population fleet, 6 battleships, 24 cruisers, 42 destroyers, 72 corvettes, probably the second most powerful fleet in the entire galaxy outside my own personal fleet, perfectly designed to combat all of the federation's enemies (point defense on every corvette, fighters on every cruiser, 2 battleships had fighters, 4 had nothing but tachyon lances). They dismantled it the instant they got control of the federation and replaced it with a bunch of worthless fleets with some tiny amount of corvettes and cruisers each. The fuck's the point if they get rid of it all the instant they get control? I had to pay for all of it myself, goddamn, plus, 100 out of the 300 population involved in that was provided by me out of my own population, so come on, I'm rich and powerful and you people ain't, let me help you.
EDIT: And you know what, more AI complaining, I also had to personally destroy the entire prethoryn scourge myself despite the aforementioned federation fleet being perfectly prethoryn busting and getting into control of my allies, all of whom were getting completely walloped by the prethoryns with me being the only one with no risk associated, because for some reason they don't consider prethoryns an actual threat even though they're the only threat at all.
EDIT 2: Also, every time you delete a federation fleet design it resets to your standard fleet UI instead of the federation design UI. Completely awful. Don't bother with federations.