It would certainly make sense if the Vasari had some resistance to PM's, but as for advent, I would be okay with the Guardian having the ability to resist phase missiles.
As for the rest of the stuff by Seluceia, I agree almost entirely.
GRG logically should do more than just damage. I really have never understood why on earth this ability kills movement. This seems more like a slug that might punch straight through your ship and keep going than something that would hurt your engines. That said, either mitigation or armor should get debuffed if hit by GRG. Ideally IMO, you would have it deal minimal damage to shields, but most of its damage to the hull. That's probably too much of a change, so I'd settle for a 3/6/9% mitigation drop from a hit of this.
Animosity... Makes sense for it to deal damage as it logically is the super-sized version of Ruthlessness. I'd also be fine if it upped the power of the weapons on the Radiance or something. Animosity needs something else.
I'd never thought of that for Clairivoyance... Great idea though to have it increase bombing damage as it does make sense. If you can see a planet and those on it, you'll know what and where to bomb to maximize damage to infrastructure and loss of life.
Phase out Hull is an interesting ability. Back when I first started suggesting that it heal/damage based on who it was aimed at, but have it instead scale with something like 100/200/300. Surprisingly, the idea caught on, but now it just does a flat 200. Regardless, it makes sense that shields are going to be affected if you yank out the ship that was generating them but not the shields. Alternatively, if you let the ship know ahead of time that you are going to phase it, it would probably be able to deactivate its shields and charge them during the interim so that its ready for combat when it returns. POH is one of the most versatile abilities in the game. It interrupts, pauses, damages, and heals.
Dominas have always bugged me that they need to face their target. Get rid of this, and they suddenly become far more powerful. Channeling should be fine, but the turning is a annoying.
Ruthlessness as has been discussed elsewhere has always struck me as weak... If it stacked 2-4 times it might be better. Sure, it would only be 3-6 DPS, but that is across your whole fleet. Alternatively, increase its range perhaps?
Inertial Field (the enforcer ability, I can't remember the name) just needs more range IMO. I've never really used it that much, but it just seems to small for my taste. Someone who's used it more is welcome to correct me.
Wave Cannons. These weapons... I don't really know how to fix them... In the mod I'm working on, I'm making them act as armor breakers, but that is probably overdone. Just something to make them worth while... Pulse Guns at least get the Orky, but wave cannons get capitals (which aren't there for their DPS) and Enforcers. Perhaps some buff to the research? Lower its tier? I don't know... Something...