I like the Advent Rapture capital Ship. When you get to level 6 you can use the Domination ability and convert enemy ships to your own. I just completed a game to test how many ships you could convert and got a fleet size over 6000. I used 16 Rapture capital ships and would go into a battle and convert their entire fleet and destroy what couldn't be converted. I only needed to fleet upgrade enough to be able to create enough initial slots for 16 capital ships (16x50). Then I just began converting enemy ships. This keeps your fleet upkeep costs down.

One word of caution. Create any ships you want before your fleet capacity number goes negative. Once it goes negative then you will not be able to build your own ships. I encountered this when my missionary vessel was destroyed and I couldn't build another because my fleet capacity was -2000. I had to use Domination to convert a Vasari Jarun Navigator to be able to acquire planets.

In the end it was massive domination as I had a fleet 3 times the normal limit of 2000. When you have 16 Rapture capital ships going into a battle it is nonstop clicking from ship to ship converting enemy ships as the cooldown period for Domination is only 60 seconds. One word of caution, disable the other abilities so they don't use antimatter automatically. This will save all the antimatter for Domination.