I stand with gunny on this one, there is definitely no "best" ship."Best" is purely preferential, the Atlas and the Prometheus are both shite in combat, but without them really big fleets are harder to manage. The Astral lack a lot of firepower but it brings so many fighters to the party that its individual combat is null, as for the Gemini, 3 individual Gemini are a much easier target for any frigate than a single super carrier. The Paragon is all about it's ship system, and advanced shields, it can literally take hits all day, and then shoot a lot of hot plasma right back at it's target. The Onslaught in one on one combat beat practically any other capital due to its massive forward firepower and its high armor, unless the onslaught is distracted by something (ie not one on one combat) I've never seen an onslaught lose a fight to a conquest. As for the conquest it is absolutely SUPERB at hunting down anything smaller than it, cruisers beware where the Conquest tread. And my least favorite ship the Odyssey is an excellent flagship for a well rounded fleet, bringing a flight deck for fighters, and still being strong enough to fight pretty much any ship head to head, although use caution when that other ship is a paragon or an onslaught, or hell any capital ship.
All that said, my favorite capital is the Astral, personally i love fighter fleets and seeing hundreds of little fighters buzz all my enemies to death. With a proper fleet of fighters supporting it, the Astral can literally beat anything.