So, looking for something more than just line up the Feds against the Klinks and letting the phasers fly when playing Klingon Armada, I went to the Federation Commander webpage and went looking through their scenarios. I opted for "The Mighty Hood Goes Down." (It gave me an excuse to pull out one of the planets I had made a couple years ago.)
I basically just swapped the rules, leaving the ships and victory conditions as is and played a game with the boys tonight, with each one of the older three controlling a Klingon Empire ship apiece and my youngest rolling dice for me controlling the USS Hood. I think that to use it with a reasonable outcome for the Federation player the number of turns needs to be halved, making it five turns rather than 10. This isn't too far out of the realm of feasibility as it seems that a Klingon Armada turn seems to account for about twice the time a Federation Commander turn does (as evidenced by photon torpedoes being able to fire normally each turn rather than every other turn). Our game lasted five turns and resulted in the destruction of the Hood, though that is really rather inevitable, but wouldn't have lasted that long if one of the Klingons hadn't committed a navigation error and left the board in turn two. (No, I didn't let him go back and change his movement orders, won't learn otherwise.)
Even if using only five turns, I think a standard CA would have a tough go of things against three cruisers. It seems that the best option would be to hang out at long range until the drones are depleted and try to cherry pick a D6. Only problem with this is that Disruptors are longer ranged than Photon Torpedoes and Phaser-Is. I was lucky in that drones did not do much damage, and the suicide shuttles never made it to my vessel. I was surviving fairly well using the repair team special rules until I decided to turn in and engage with torpedoes. Ships die much more easily in KA than FC, so I'm also considering swapping the CA for a CC to give it a better weapons loadout. Though a BC would be interesting too. Swapping in a Fed DN would be entertaining as well. Overall though I think using the FC scenario for KA play worked out reasonably well, and will be better by shortening the turn limit. Other than that I don't think that there's really any other tweaking that needs to be done. In this scenario in particular, the Hood is going to be destroyed, it's just a matter of whether or not it can hold out for the transports to escape and if it can take a ship or more with it.
Might get some pictures posted tomorrow.
Oh, and though I lost my ship, it took a D6 with it.