Rapture Battlecruiser.
It becomes the flagship for my fleet and remains so throughout the game. I find I really don't need more than one, ever, instead I get doubles of Halcyons and Radiances.
I always get and give priority to Vertigo as it's cheap and has a fast cool down. You can really hamper your opponent when all of his cap ships and most of his cruisers are hit with this.
Next is Vengeance and works extremely well in self targeting usage as the Rapture is a lucrative target.
Concentration Aura is good, but Advent strike craft are already a force to be reckoned with, and unless I'm building alot of Drone Hosts, I put my points elsewhere.
The only con I've noticed with the Rapture is that it's not so good under heavy fire. It can dish out pretty good damage but can't take it. In fact, I've found the Rapture gets in trouble faster than any other advent cap ship except maybe the Progenitor. But once I have it covered by a pair of Radiances, and backed up with a Halcyon and a Revelation or a Progenitor, it dominates the battlefield.
Oh, and speaking of Domination it's a truly wonderful late game ability, especially when you have Disciples stealing antimatter and giving it to the Rapture; all of a sudden, your enemy is down 5 or 6 heavy cruisers and you're up 5 or 6 hehe!