I have to disagree with Angelus' call on the Omega. In terms of the four main races, even with the Armageddon upgrade, it's still the weakest. Heck, I'm not even sure it's the best within the EA.
It can probably be safely considered to be better than the Orestes- although not the 2241-49 Dreadnought from the EMW book, with it's amazingly non- boresighted medium laser.
the 2249-61 version of the Avenger is also battle level, and, well, basically a specialist ship. Fighters are still not that lethal.
Footnote for Earth Civil War players; recommission any derelict Artemis you come across. One of those and two Hermes wiped out a seven flight fighter attack force for me this afternoon, and it claimed four of them. And main share of a Nova. Incidentally, pretty much every EA battle choice except the Avenger has antifighter. Most of them turreted.
The Command Hyperion is, well, an EA command variant. it does not have the survivability to be worth it's level.
The Pulse Omega is a gap filler; you use it to support more conventional ships, on it's own- I have seen it used successfully, once. As bait.
The Apollo needs a fleet structure to perform in, to escort it and do the grunt work, but given that, it can justify itself. I use it with Flash, not for primary kills, but to kill off smaller craft and coup de grace larger damaged ships. It is artillery.
In terms of prime EA Battle choice, is there really any doubt? Marathon. it is still a shade fragile, but it is fast and hard hitting.
The problem with the 'Wall of Omegas' strategy is simply- what's the enemy going to put up against them? As Dilgar, say, I would split three of a 4-Battle force down Raid-Skirmish-2 Patrol, get 2 raid for the other, five Targrath three Omelos six Jashakar, I can maneuver a lot faster and more fluidly and need actually hazard boresighting on only light ships. I could expect an average two targeting locks a turn, with far more flexible long range and heavier close-range firepower. I reckon I'd lose two Jashakar and get one Omelos, one Targrath mauled, for four Omega kills. I would see that Omega wall coming and think 'easy meat.'
Then again, I reckon the early EA list is lethal enough to hurt the Minbari at anything much less than the absurd odds from the set scenarios, the Third Age list is more or less balanced, and the Crusade list is paralysed by it's own dead weight.