p.s: My log says I spent 1034 turns in armory. Bug?
Oops. Thanks for letting me know, that's a bug. I just looked and the turn records skipped over Archives, which was an unplanned map, so it recorded your Hub visit turns to the Armory. There's no impact other than this; I'll have it fixed for the next release.
The Network Hub message isn't 100% clear, since it's in theme, but in Alpha 7 there's a place you'll be able to learn more specifically what that does if you can't already guess. It can be quite useful (hence the heavy defenses). True there are so many systems now that guessing these things can be difficult. For now I've changed the message to
ALERT: Network intrusion management efficiency reduced by 5%.Ally builds will be more viable in the future. Still working towards that, but yeah Enhanced Grunts can carry you pretty far if you take them back to the main complex. Though controllability is not likely to change--allies are in most cases meant to be just an autonomous boost to your capabilities, since we don't want to really get into micromanagement. You either have them or you don't, and you can indirectly control how things turn out via their composition and supporting parts like remote shields and hacking. (It would be nice if you could set some overall tactics and allied AI would stick to that, but the AI is not really built to handle such a thing...)