I have played all 4 races extensively online. In each race, I have gotten up to their most powerful dreadnought (got bored with the borg before I got a cube). I think alot of the complaints are coming from Fed players, and there is a reason. Its not that the cloak is now unbeatable, that just adds to the problem really. The fact is, the feds are slightly underbalanced.
Feds have the strongest shields, right? Ya, they can usually take 1 or 2 extra shots.
Feds armor is second strongest. Again, fed armor can take 1 to 2 extra shots.
In exchange, we give up maneuverablility, speed, stealth, and power.
Some people say that feds have better power output. That's true when a fed ship is underloaded. Shields and heavy weapons suck up that power. Consider, a photon takes 8 power, deals out about 9 damage. K-Photon takes 6 power, deals out 6 damage, and takes half the time to reload. But Feds have the "mighty" quantum. 13 damage, 10 power. Polaron does 12 damage, 9 power, and recharges slightly faster than the quantum. Ahh, but the quantum has burst fire, that now happens alot less. While the polaron's shield bypass seems unaffected. Oh, but we have the pulse phaser. Wich was almost useless before the patch. Now it's completely useless. Phasers are generally the same as Klingon disrupters.
So, whats the advantages of playing Fed? The ability to absorb 4 to 5 extra shots, if your lucky. 180 degree primary weapon mount, wich does generally give us an edge in the light cruiser to heavy cruiser department, but wich is lost in the battlecruiser and dreadnought, and doesn't exist in the frigate and destroyer. Disadvantages? Lack of weapon variety, power consumption vs. power generation, power to damage ratios, speed, agility, stealth.
Now, the Romulans have been brought up to par. Before, it was the Klingons who had the edge because of superior power to damage ratios, and reload rates. Hasn't been long enough to see if the Romulans will be contenders, but I know this, the Feds weren't to begin with.
Of course, many of you will say I'm just a whiney Fed. Maybe I am. But I've played all 4 races many times. I've learned how to fight as each competently, if not mastering them. Before the patch, I would say the best ships were Klingon, Borg(not counting the cube), Fed, and Romulan. With the patch, I'll have to play as all 4 races again to find out how things stand, but I don't see the Fed climbing the ladder.