One thing that immediately feels a little lackluster is the Covenant's capital ship abilities. I imagine they're still a work in progress, but I've been thinking about what can be used to fill in some of the gaps. As a caveat, I'm just throwing out ideas here without thinking how they'd be balanced/if they are balanced/etc.
I get the general sense that the Dev Team has purposely tried to avoid Fleet-wide command and control buffs, like weapon range and weapon cooldown, which to me makes sense. I don't think the Covenant need those.
The assault carrier has some free slots (1? 2?) I forget. It has a handy planet bombing ability, which is probably fine, but the level 6 ability is a little wanting. Its level 6 ability is, as far as I can tell, the same or substantially similar to what the anti-strikecraft corvette has. Given that we've seen assault carriers disgorging swarms of fighters in the lore, why not give it some sort of Advent-esque Anima Tempest style ability. It would allow you to make the anti-strikecraft ability a normal ability.
In another thread, I mentioned some of my misgivings/concerns about the Super-Destroyer, in particular that the refire rate is so long on energy projectors that its massive damage doesn't exactly shine through in a huge battle where things die incredibly quickly. To some extent, the Super-Cruiser suffers from this same problem. It does great damage from a great distance, but it generally seems to fire once before it, in EVE-parlance, gets alpha'd and dies in a horrible fire.
I have two ideas for this. One, the less OP idea, I think, would be to give these ships some sort of Overload Weapons ability. Have it do something like increase the refire rate of energy projectors by X% for 20-30 seconds or something, but keep it on a very, very long cooldown. I don't intend something like what the Tector Star Destroyers have in SoaGE where it's pretty much always active. I mean something that gets used once every 5 minutes and when it does, it doesn't do anything drastic, but the SD/SC can get a couple more volleys off before it dies. As a penalty, have it draw power from engines, or if it's possible to have an ability do damage to shields (I know abilities can self-inflict hull damage).
The other idea is more of something along the lines of the standard AoE volley ability. Similar idea, but on a less grand scale. Have the ability fire energy projectors at random targets, but keep its scale small. Level 1, 1 target, up to level 3, 3 targets. Similarly long, non-spammable cooldown. Once-per battle type ability. Just have it do approximately the same damage that normal energy projectors do. It's entirely conceivable that the SC would need some cost/fleet supply increases if it had this ability because it would be pretty easy to spam these and AOE fleets with huge volleys of energy projector fire (especially when coupled with the damage propagation abilities).