Most Capital Ships aren't so much about their combat abilities as they are their special abilities that they earn as they gain veterancy. The Dunov and Akkan are both Support ships, which makes them more reliant on them than a Battleship or Carrier.

The Dunov is good at direct combat aiding. It has Shield Restore, which gives a significant boost to the shield of a single ship in the area that you select, a near instant 350 boost can help another ship survive a death strike or escape a combat area. The EMP Charge can do a nice bit of shield damage and drain some Anti-Matter from an enemy ship. Magnetize is a mean ability that can kill nearby fighters easily. And finally Flux Field makes all the nearby ships abilities much cheaper to use in Anti-Matter. Altogether, it's a good ship to have in the fray.

The Akkan has some different abilities that are no less useful. It's most important ability is probably Colonize, which allows you to not have to worry about having to tow around a Colony Ship that is bait for half the enemies in a system. The Ion Bolt is a more direct ability, it temporarily disables an enemy and makes them an easy target. Targeting Uplink increase the accuracy and range of friendly units in the area. And Armistice disables nearby enemies but they are invulnerable to damage. It's a better ship to have a bit behind the fighting, but very valuable for being able to colonize.

They're both support oriented Capital Ships with different abilities. They have similar stats, the Akkan is a big stronger but neither should be going toe to toe with an enemy Destroyer or a large group of Frigates alone. Personally I like the Dunov for it's Shield Restore, but the Akkan's ability to Colonize for a fleet on the move and the Ion Bolt to stop an enemy from running are great things.

A good fleet will have both though and a mix of ships. Kol's are good for direct combat. Marzas are good for planet bombardment and limited direct combat (preferably behind the Kols). The Akkan and the Dunov are good at supporting the other Capital Ships and Frigates. And the Sova can provide fighter/bomber support as well as it's Embargo abilities.