Lately with advent, I typically end up with something like this, although Dominate tends to mix things up a bit (note: this is against the AI - I can't afford the addiction of multiplayer right now):
Cap Ships:
Mothership, Rapture, Halcyon, Revelation - built in that order typically.
Mothership - All abilities are fantastic but after 1 level of colonize, shield is the first pick and it gets upgraded at every opportunity after that. It's great at first, almost unfair when Advent shields get really nasty towards the end of the game.
Rapture - Usually comes along at about the time I've started adding drone frigates to the fleet. All skills are winners but Revenge is great at level 2 and up. Against the AI, I like to send it in first and let everyone acquire it as a target for a while, then the rest of the fleet follows and starts healing it up while it returns twice the damage heaped upon it on top of whatever it's actually dishing out without Revenge. The passive strike craft boost is great too.
Halcyon - Repel gives a huge edge in massive strike craft battles, and the cooldown reduction ability is phenomenal. I've actually started saving adept drone anima for last. It's nice but doesn't do as much for a large fleet. The Halcyon tends to come along as I'm adding my first Illuminators.
Revelation - This would actually be a strong early cap pick but it tends to top off the fleet in my games. Mostly used to distract problem caps with Revelry, check on potential targets/agressors and to kill planets fast and rather horrifically.
Cruiser/Frigates
Assuming a fleet of 100 (not counting caps).
15 support cruisers (5 of each type) - I tend to micro some of these.
10 Disciples - they become quite survivable with endgame technology and the antimatter leeching keeps the abilities cranking
20 Drone Hosts - Usually with 1:2 fighter/bomber ratio.
20 or 35 Illuminators - Huge, multiple target firing arc. Illusion makes it hard to strip shields off of one before they've been periodically restored,
(if 20 illuminators) 15 Defenders - I've been messing with these guys more lately. They're not bad but the Halcyon does the job against fighters once antimatter becomes easier to restore. I think defenders are more suited to planetary defense as they're tough and deal with fighters well.
20 Crusaders - I don't have much of an opinion of these as it's hard to see what's going on at this point in the game but the attrition rate definitely seems to drop severely once the first 10 or so crusaders are in place.
