BFG is one of thsoe games that's strength is in size.
A full 2000 pt fleet can easly be done in 20 ships, and that's it, that's all you need. Sure, Eldar might run you 30 or 40 vessels, but then again, you rarely even see a 2000 pt battle.
Necrons, on the other hand, might only run you about 10 ships for 2000 pts.
Technically not all of the 40k armies cross over into Gothic.
The Imperial Navy would technically be the IG. They have the largest list of possible vessels, depending on different fleet deployments (each Sector fleet for the Imperium is allowed certain vessels). Their strength is in flexibility, as well as a great deal of torpedo fire and decent all-around vessels. Because of the large availability and variety, this fleet could run you the most ships, to always have what you want handy.
The Space Marines have their own fleet, and each chapter works exactly the same way. The Grey Knights are an exception, and they're bonuses are strictly agianst Chaos. Space Marine ships have strong but short range guns, impressive speed and strong armor. Their role is a fast hit and run, dropping troops planetside. They have VERY few choices for ships, only a single battleship, one cruiser, and three escorts (plus the ability to take imperial escorts and upgrade them with SM crews). However, they also have the Venerable Battle Barge, which allows any one Chaos or Imperial capital ship to be considered a relic from the Golden Age and be used as a flagship.
Chaos has one fleet, though the ships can be Marked in a similiar fashion to troops, and you can't mix and match... the same way a Chaos 40k army would work. Chaos has a small selection of ships, as they stopped making vessels after the betrayal, but their ships are faster and better armed than the Imperials, as they have tech the Imperials can no longer replicate. They have arguably the best carrier in the game, and their gunships are unmatched for cost and lance support in weapons.
Tyranids have a fleet. I know very little about it, but I do know that they're unmatched in boarding actions, and that they're an extremely modular army, with only one of each type of ship but the ability to customize each.
Dark Eldar are fairly similiar to Tyranids in that everything's modular. They're fast, fragile, and good at boarding.
Tau has two fleets... one is 'official', the other, last time i checked, was created by Forge World. Their ships are fairly weak on their own, but their strength is in massed firepower, being able to throw swarms of drone torpedos at the enemy. They are deffinitely a fleet that needs large groups of vessels.
Orks have a fleet. Their ships are random; guns have dice rolls each time you fire to see the strength of the weapons. This gives their guns the chance to be extremely powerful, but also a chance to fizzle. They're decent in close combat, on par with space marines.
The Eldar have two fleets; the Corsairs, or pirate fleet are the ones in the main rulebook, whle the Craftworld Eldar are a closer match to the 40k army. They can be combined using special force organizations... the Corsairs specialize in horde fleets of small escorts that fly around like Tau suits, while the Craftworld Eldar have impressive cruisers and larger vessels.
Necron ships are 'broken'. Very powerful, great armor, impressive if not amazing speed. Their penalties come from being very expensive, not having many choices, and they give back ALOT of victory points if they get damaged or worse, left behind.
I -think- that's everything.