This is for constructive feedback if you wish it. If you want to post your opinion it is perfectly fine, but lets not use personal attacks on anyone.
There is no answer for the carrier/cloak combination in this rank on the Fed side. Two premade teams could be another case. However, this is based on PuG versus PuG in most* cases.
You can group up as much as you like but when you mix battle cloak in with 3-4 carriers, the map becomes litterally an infested area of NPC type pets that knick and pick at you causing you to constantly stay in combat and giving no rest. Your screen will become a virtual junk yard of Klingon ships(For all I know these ships could be junk to Klingons, but they did do well against my Cruiser). FPS is another issue in these cases.
Viral Matrix is used by nearly every ship. You can counter it with Science team for a little bit, but mixed with cloak, the only Klingon that wastes VM is a thoughtless one. And most Klingons I have know are smart enough to wait. VM is another issue on its own however.
After this point, the federation has no true counter to the dozens and dozens of ships flying around syphoning, shooting, healing, etc.
The targeting issue is not so much as it is the ability to for the DPS types to also cloak in and out of these battles at will, giving DPS types an even larger buffer to use their preferred skills at their preferred time. While a Federation player is left to hope that there are no cloaked ships, and a Klingon feels assured.
Klingons get more customization, mainly due to the fact that Klingons were pushed out the door as fast as Cryptic could. The ability to fine tune your BoP is an amazingly useful ability. And if the 4 crew slots are something you cannot deal with you have other options. I hope this is not nerfed in any way, this makes the two sides more unique(other than the fact that everyone uses the same things on their BO )
Constructive feedback to this? Nothing is perfect, so don't pretend things are.
I do not envy the beta testing Klingons have to do after the release. However, things must be balanced properly... so lets keep things civil.
That means you too federation players. Don't go posting when you reach T5 "OMGKDASFJ NERF" Lets just talk it out, and you can usually pick out those who care about the games future and those who just want to secure their own domination even at the price of the games future.
One of the major problems is targetting. It is very difficult to target carriers amidst a fleet of smaller ships. I'm not just talking about tabbing, but actually clicking on them can be difficult as well. This is the same problem that we saw from fedballs mine-spamming. It's a UI problem, not a game balance problem but obviously it leaks over. In pvp, tab should always select players first. This goes for ground as well.
Klingon players saw this sort of thing since closed beta via the Fed ball. The difference is we have cloak to be able to pick and choose our battles. Cloak was a big factor in how we dealt with the Fed Ball.
But, Feds don't have this at t5. Hm. Yeah, a dilemma. I know what it's like when your screen is filled with mines and every ship is unloading on you with phasers. It's pretty overwhelming.
One possible response, and one used in SFC, is the ADD, anti drone defense. It was a weak missile/phaser system that was very rapid firing and auto-fired when drones or fighters got within a given proximity to the ship. Very effective in most cases though by no means perfect.
Maybe there could be a new weapon loadout for the devs to make based on a similar principle. Like a phaser system that fires only on fighters/shuttles and it set on auto fire. The Aegis Defense System?
Honestly I think it's a taste of their own medicine from a purely tactical standpoint. The Federation side took advantage of an inherent UI problem and began mine spamming to prevent their ships from being targeted. The end result was Klingons using what they were given, fighting smarter, and countering with the "cloak and hunt" tactic. In terms of battle, I say they just deal with the NPC ships they way the Klingons have had to deal with the Fedball minefield. If both sides are smart, they will simply develop a metagame around these tactics and the world will be a happy place filled with glorious battles and "MAN I can't believe we won/lost that!"
Now before you start flaming, notice where I said "inherent UI problem." I also agree that the UI needs some work in the targeting area. There were some improvements in beta with color schemes and the ability to tell enemies from allies. but I find one major problem with the way things are now that supports what the OP is talking about:
You cannot always target your closest enemy. If a mine is .05 KM away from your closest enemy player target, more than likely you will target the mine if your camera is not angled properly.
Two of the things I enjoyed about Guild Wars was the ability to hit either Alt or Ctrl (depending on how one binds it) and being able to see all enemy or NPC targets at a glance. The second was the ability to hit one button and target my closest enemy. Now if that enemy was an NPC pet, it got targeted and I manually adjusted my target choice to compensate. But the way things are in STO's UI, target selection seems random and based on nothing more than "oh look, here's a bad guy" no matter how close they are to you.
I'm not sure if that'll solve *all* of the targeting issues, but it is what I've seen thus far in my adventures in deflating the Fedball.