looking purely at TEC, I break them down the following way:
Kol: big guns, lots of health
Marza: lots of missiles, lots of health
Akkan: I don't need to wait for that stupid colony ship!
Dunov: Shield repair heals more shields than any other early-game unit starts with. I take it as my 2nd or 3rd capital ship if I get one, or pair it with some Hoshiko cruisers and call it an auxiliary fleet.
Sova: essentially unopposed in the early game, is GREAT to have at a reasonably high level when you start to churn out carriers.
I tend to start with a Sova, Kol, or Marza, as they tend to pull their weight better in combat. Sometimes I start with an Akkan to go for capturing speed and the tactical advantage of not having to wait for the ceramic teacup of a colonizing ship.
I don't ever start out with a Dunov. Mid-late game, however, it is well worth the resources.
Most of the Dunov's and the Akkan's strength can be attained early on, and there is some improvement later on. With the Sova, Kol, or Marza, the name of the game is to get to tier 6 for the uber-power, and unleash the pwn. A ship healing them while they are doing this compounds their usefulness, without having to go through the laborious, mildly dangerous, and extremely boring process of leveling a capital ship from cold to juggernaut.
Additionally, the system for capital ship experience is not how many ships that capital ship personally destroys, but the sum of the values of enemy ships, divided equally among your capital ships below level 10. In this way, once a capital ship is at level six, it is very smart to pair it with a Dunov, as the first cap. already has its best power, and the rest is just a side show, so it doesn't lose much power by splitting the experience points. What it does lose is offset by the shield recharging and countermeasures that the Dunov packs, such as the EMP or flux field (which is tier 6, very nice, but a pain to get to).