I have to agree with Jan when he points out that it takes a lot of time to build the big ships. As it takes too long if you have an enemy constantly sending in fleets of small ships you won't survive until you have even one of the bigger ships and if you have one it is likely destroyed by uncountable small ships. So what to do about it? Of course you will also start building lots of small ships because there's not really a reason to wait and tech if the cheap and small vessels are able to do the same job.
I'd appreciate a solution preserving the value of small ships but forcing you to build also bigger ships. (If you just needed to build a bunch of Sov's to win, FO would be the same as stock A2.)
More effective special weapons might make the big ships more attractive to build.
(E.g.: If the Dampening Missile wouldn't only disable one random system for five seconds but every system for the same time it would be worth the money and the time you have to invest into a Breen Battleship. - I know, this is very yucky

)
The rebalancing Optec mentioned is already a very good step to get diversified multiplayer battles. I think there will be a good solution to bug/bop/saber/shrike-spam.