im sorry, i mistyped, the evacuator has more damage, hp, and shields and a skill that is actually useful against militia, the only disadvantage it has is that it is even slower than the akkan, but that doesnt matter since it can actually KILL its foes (unlike the akkan)
That's why I like it for the early game. A levelled nano dissassembler is a very potent weapon in the small-scale early engagements, because it strips a lot of armor and also does a nice bit of guaranteed damage, which can help it fend for itself better than the akkan. It's a small enough ability later on that it can go unnoticed, but definitely helps it considerably in the early game. Also, it has a bit of punch, so you aren't wasting the flagship bonuses as much as you would be on an akkan.
EDIT:
although it lacks the ability to keep an enemy locked from hyperspace, making assassinations against ships more difficult (curse thee AI, curse thee Derekor!)
You must have missed the other one of the Evacuator's abilities, gravity warhead, which "slows the movement of targeted enemy ships and prevents them from entering phase space." Combined with the nano-dissassembler, the jarrasul comes with better abilities for assassination than the akkan.