I know I could break this up between the two shipyards but we all know one is just a KDF mirror of the other in its function.
Let me start by saying that I think the Odyssey is an amazing ship and in a lot of ways so is its KDF sister. However, there is one console that can easily be tossed out if not for the set bonuses and that is the Aquarius.
This ship has similar armaments to an Advanced Peregrine that can be launched by a Heavy Escort Carrier or the Atrox. It does not seem to deal any more damage than a single Peregrine and if it does it maybe deals 1.5 times the damage. Considering that with a single bay you get SIX Peregrines that means they are vastly superior to the Aquarius.
Now I realize that the Aquarius survives combat a lot better than the fighters, especially after its AI changes, but the point is that being so much larger and requiring an entire CONSOLE slot to use (which Peregrines do not) that it should be a fair bit superior to at least a single launch of Peregrines.
So my suggestion for the Aquarius is that seems how it has a Point Defense cannon, why not give it Cannon Scatter Volley III, Torpedo Spread III, and make it behave as if it were in intercept mode. Also bump its damage a bit so that its weapons would be the equivalent of Purple MK XI or at LEAST X with a focus on Accuracy. Make the Aquarius really have the role of cleaning up all the little ships, mines, and torps pestering the big tanky Odyssey.
Next allow the Aquarius to be "Giftable" just like the Tal'Kyr and finally that Console can actually be worth having. Right now NO ONE buys the Tactical Odyssey for that console they buy it for the power setup and that third Tactical Console Slot. Make it more worthwhile and you can fix this.
For the HoH'SuS on the other hand... It still needs its weapon power boosted as previously described for the Aquarius but considering what it is supporting it should have a different setup. Give it Chroniton Torps or Photon Torps (if you want to be more canon). Transphasic Torps are a SERIOUS joke and I am pretty sure by now you all know that they are worthless. On top of that they make no sense. When did the Klingons suddenly own Transphasic Tech and treat it like their big deal?
Next give the HoH'SuS Cannon Rapid Fire III and Tractor Beam III. It is supporting the Bortasqu' which needs its enemies to STOP MOVING reallly reallly bad. It is nice that the HoH'SuS can deal some damage with the new setup but stopping the enemy will go even further to really making a difference for the Bortasqu'. Unlike the Aquarius this one should be in Attack Mode always going after your target and should NOT be giftable.
You could also have the HoH'SuS battle cloak but I am not sure it is really worth bothering.
Neither of these pets would really make carriers worthless because they can field far more pets to much greater effect but it would make these pets ACTUALLY VALUABLE. It would put more hurt on the Multi-Vector pets but those really need an upgrade as well.
I know your trying to make things better but I have a couple things to say.
If you want to the Aquarius to survive beyond the first volley don't give it two strong aoe abilities. As soon as it pumps out that first spread and starts spraying those cannons unless you know you or someone has strong threat against the targets. That little Aquarius is going to take threat and get gang banged.
Why does the Aquarius get *gifted* but the Hoh'SuS doesn't? Already enough reasons for someone to buy a Odyssey, its superior in every way over the Bortasqu', but one should also get another free vessel with the Odyssey and the Bortasqu' shouldn't?
My big delimma is wether or noy the Aquarious would be worth getting the tatical oddy vs. The galaxy dread. or the eingeering oddy
Aquarious shouldn't factor into the Tac oddy's consideration, it's a neat toy but the selling point is that the Tac Oddy does more damage over a short period of time than any other oddy variant. The aquarious just helps it win a little more at that game.
The Engineering Oddy has the "best" console and can adjusted it's play-style on the fly. It's the most popular of the trio because of this.
The Dreadnought is more for Tac officers than engineers. The cloak and Spinal Lance combine with Attack Pattern Alpha and Fire on My Mark for one of the nastiest Alpha strikes in the game. Chase with HY quantum torpedoes and you've probably killed your target. If not it's still better than the RA cruisers.
P.S. The Sci oddy can actually do the most damage out of the three variants with it's sensor analysis, but taking advantage of that ability requires staying on a single target for a long time. You can not target your team mates for heals and can't switch to a more injured target without running the risk of losing the bonus. To me that makes the claims of it being "over powered" ridiculous, any one in a cruiser that won't do these things to maximize the team's chances of winning is probably not that threatening any way.