The problem with the feds is not about weapon mass limits(though the nebula is horrible), or even engine mass limits. The problem is power consumption and hardpoints.
In the Battlecruiser and Dreadnought classes, the feds don't improve. they only have 3 fwd firing primaries. Only on the Sovereign is there 3 fwd heavy hardpoints(not including the defiant here). Vs. the neg, wich can mount 5 fwd primaries and 2 fwd heavies, the Warbird wich can mount 5 fwd primaries and 3 fwd heavies, or the Sphere prime wich can mount 4 fwd primaries and 2 fwd heavies(not including the slightly off fwd/side heavies). Yet, for mounting on average 2 less primary weapons, there is also no real energy surplus. The neg, sphere, and warbird has plenty of spare power when using the legendary officers. With battlecruisers, its the same deal pretty much.
The fed ships suffer from a lack of power surpluss, less weapon variety, and inferior power to damage conversion. The battlecruisers and dreadnoughts also suffer from lack of fwd weapon mounts. Additional side mounts DON'T make up for this, and really is a disadvantage overall. I tried mounting the side mounts on a fed ship. But with their terrible turn rate, and lack of power, all they did was suck up power from the fwd weapons.
Stronger armor and shields don't make up for this either, because they aren't that much stronger than Klingon equivalents. The advantage translates into maybe 1 to 2 extra shots can be absorbed, but with the most enemy ships, that's not a problem at all.
The patch didn't really hurt the feds too much, it just fixed problems with the romulans, and brought them to an almost equal footing with the Klingons. The problem is that the Federation is just not balanced well at all.
I have played all 4 races extensively online. I know their strengths and weakness's. And the feds are the weakest race I played. The only tactic that really works with the feds is too mount all am mines. Of course, to most of you, I'm just a "whiney" fed. To that, I say, try actually flying fed for awhile. Get a fully loaded sov, then take on a human neg. The only time I won against a neg was when I tractored him and mined him to death. Every other tactic I used failed horribly, most times I couldn't even penetrate the shields before I was down to half a hull.