Imperial Navy and Chaos are well balanced, I believe, though they each have ships that needed work (Styx's cost, Tyrant etc) The other fleets though, are not really. Orks are just poorly thought through, Eldar in the BBB win if there is terrain, and lose if there isn't (Check out MSM elday, in the OP of the main BFG:R thread by AfterimageDan, it's alt rules that balance the fleet way more. credit to Horizon and Sigoroth) Space Marine are just too small a fleet, so they're more fringe, and the strike cruiser have been given way more options since inception now, I believe. Dark Eldar needed a lot of work too, with only too ships. Tau had only 1 real fleet option (AC spam) when they were initially created. The list goes on. Tyranids, they're just broken (Not the powerful broken) with several iterations of their rules to try to fix them. It's possible to have good games with the fleets, and the imbalance isn't ALWAYS horrific, but there are a couple glaring ones here and there (Eldar MMS in particular strikes me, as I play Eldar).
Having said that, it's not as imbalanced as 40k, I believe. You have no 3rd and 4th edition codecies playing off against 6th edition anything.