They both preform tottaly diffrent purposes, and can't really be compared that way.
I get more use out of the Ghost Ark myself, as many people consider the Doomsday Ark to be subpar.
You really should consider your entire list. The Ghost Ark is first and foremost a transport. It can also repair fallen warriors. It also has Quantum Shielding, and living metal as well, boosting it's durability quite high.
It is quite expensive points wise, at 115.
The Doomsday Ark is our longest range weapon, besides a Tachyon arrow, and Harp shot. It's got QS and Living Metal as well. However, it's biggest downfall is that if you move it, you can't fire it's main weapon at full power.
I would say, check out your list, and play a few games first. In the end though, I use my Ghost Arks much more, than my Doomsday Arks.
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