What sized/mission games do you play? And can you describe how a normal game goes?
I wholeheartedly support the chaos cruiser fleet as one of the most powerful - yes, all right, necrons and eldar, but for simple, low-cost, shed-loads of macrobatteries, it's hard to beat a line astern of Carnage-class cruisers firing locked-on broadsides.
I'm not sure I'd say overpowered, but the Imperial Navy has its problems engaging them. You have your own tricks up your sleeves, however - principally that bloody great slab of adamantium on the front. 6+ prow armour is nice, and torpedoes are a seriously scary weapon if used en masse. Yes, with a few carriers a chaos fleet can soak up a lot of torpedoes but carriers dedicated to fighter screens aren't flinging dreadclaws in your face, and with every capital ship packing torpedo tubes that's a lot of salvoes to stop.
The theoretical trick with Navy fleets - and it's not an easy one - is the fact that whilst a Carnage carries ridiculous firepower to one side (because a lot of it is tied up in the prow mount), a Lunar puts out acceptible firepower to both sides, and has lances into the bargain - one thing to note is that outside of prow mounts (which you don't want to be using) or heavy cruisers and battleships, Chaos fleets lack access to lances on their normal 'fighting ships'.
Hymirl, if he pops in here, knows his way around the Imperial Navy like the back of his hand - in fact he won the last BFG GT they did with IN ships. He's a big fan of the Lunar-class and the Sword-class, both of which are fantastic value for points.
Necrons and Eldar aren't too bad when taken as a whole - it's more that a fleet is either suited for fighting them or not suited for fighting them scissors-paper-stone fashion and if it's the latter (say a high proportion of lance boats against eldar) you can be screwed whatever you do.
Craftworld eldar are nasty, as is the Taros Commerce Protection fleet (which is just dirty). Tyranids are okay unless you make the mistake of letting people buy biomorphs freely, at which point they become ridiculous.