I like the Anemoi and the concept behind it quite a lot.
The fragmentation of capabilities and purposes into different classes of vessels is pretty well justified by the strategic and tactical necessities of each warship to be as efficient, light and snappy as it can be, given its own purpose. To that end, compromises are inevitable, and if the Anemoi is amazing to the GTVA in its huge freighter capabilities, maintenance, hospitals and so on, it will obviously lack in power and attack/defense capabilities.
This fragmentation is both the GTVA's strenght and weakness. By "strenght", obviously they learned not to place "all eggs in the same basket" and enter in a tactical fragmentation and modulation. If a Destroyer goes down the logistics are still intact, etc. It is a weakness because you do not have the sufficient resources to build up equal artillery for every ship (now that you are fragmenting the fleet), and so the logistics vessels become the "weakest link". But this should not be a problem since these logistic vessels are to be hidden in the vastness of space, and unless there's some remarkable cunning by the opponent, they are safe.
Also, it's these kinds of dynamics that make a plot interesting. It would be incredibly dull to have every ship like these to harbor ten fighterkillers just because "they can".
EDIT: While this is what I believe, a more apt point could be made that the WiH mission where we disable this ship and so on is "too easy", that with some fighterkillers that we needed to disable first it would become "better" and so on. But that's a whole different conversation, IMHO.