This remainds me a ton of a Halo mod for Freelancer... they have great models over there, though the developers won't allow their models to be reused in any other mod projects, aside from those established in all three Halo games (Halcyon Cruiser, Marathon Cruiser, Apocalypse Frigate, Covenant Assault Carrier, CCS Battlecruiser, etc.)
The Covie Dreadnought had a beam which traveled at light speed, at long range, and could bisect five UNSC ships in one blast (from The Fall of Reach). I suppose you could make that an ultimate ability... just make its damage absurdly high, but AM cost and cooldown time just as absurdly high. Covie Assault Carriers also carried a beam weapon, though not as powerful as the DN's beam, could still inflict catastrophic damage on an enemy ship.
Alternately, instead of using dropships for the Covenant for planet bombing, how about their gravity lift projectors? There is a cutscene in Halo 2 where an Assault Carrier uses its gravity lift to inflict damage upon Delta Halo, intended to kill the Prophet of Regret.
Seeing the Unyielding Heirophant would be epic... though to implement a mobile base like that just further tips the scale in favour of the Covenant... unless you use it as a Starbase equivalent of the Covies.
Apologies if I've repeated anything, but I don't have time to read through 1900+ posts...