Finished one run, have got a handle on how things work...
The Neinzul fleet in its entirely is surprisingly well rounded in and of itself. Although the hull bonuses are quite low, the only hull missing from the set of Commando/Tiger/Weasel is Command-Grade (which may be why H/Ks were surprisingly tough without Bombers to whittle them down). The lower max-DPS is compensated by the other two Youngling: Vultures will finish off anything in yellow or red (gosh you should see them at work), and Nanoswarms give you the time and breathing space to do the killing, as well as additional ships.
With things like exo-defense, one will still need fortresses, forcefields, and turret stuff. Pairing each carrier group with a couple of cloaker starships will save you from having to rebuild neinzul enclave starships and its Engineer attendants. Interestingly, Logistic-IIIs to boost their insane speed to 720/440 will give you much leverage in mobile defenses (ignore Econ-IIIs, you have 5 homeworlds!) The knowledge you'd normally spend in unlocking triangle ships simply get transferred to unlocking the Neinzul triangle, so we're not missing out on all that much...
I can see bigger problems versus, say, a Spireling AI since all spire ships are effectively immune to nanoswarms, and there's those Gravity Drainers... otherwise, every AI unlock that is not paralysis-immune gets eaten by a constant stream of Engineer-supported production pipeline.