Useful cap ship list
Advent
Radience: Eat antimatter, taunt fleet (force focuse fire on itself, useful when you want to save something), more armor and last but not least - cleansing briliance.
This ship is thoug, somewhat obsoleat, comparing the usefulnes of other advent ships.
Progenitor: Colonise, shield regen. Most useful advent ship ever. I usualy got 3 or more of these in my end MP game fleet. Constantly pumpping shields into the guardians, keping ships alive.
Halycon: one of the second most useful fleet ship. This is ship that i also get 3 or more at the late game. Its ability to repell fighters while damaging them and passive RoF for all energy based wepons, incuding planet bombing, makes it must have fleet ship.
Rapture: Good to have ship lategame. It'sabilities are somewhat useless untill you get massive ball rolling.
The vengeance is still somewhat nexst to useless ability that i use only when i got nothing beter to do. The vertigo is however must have when fghting toe to toe with fleet the size of yours or bigger. Its not so grate when the forces are small, but in 100+ ship swarm, 30%- to accuracy and RoF is the thing that will win you the fights.
The capture ship ability is actualy useful now, since carriers are worth spending antimatter on to caputre. 
Also, the passive damagebuff aura for strike crafts is sexy.
Vasari got the egg and marauder, but other than them, i find it rarely useful to go caps over fleet.
The TEC have tha ability to runn Dunnov/Marza battleball that constantly pumps the shields to caps. And marzas on lvl 6 are realy nasty flet killers. But the inability to benefit the rest of the fleet makes it hard to use.
In short, nothing can realy compare to the advent capital fleet.