One thing I've wondered about the champion response is whether or not the AI should be using shadow frigates in the first place.. I thought the one the humans had was a unique discovery - I always considered it odd that the AI has 100s, and not only that but they haven't worked out there's can follow you into the nebula wormholes. What if to tone down alt-response you just made it a normal exo and instead of nemesis threat fleet allow for the seeding of something else as the nemesis.
One other thing I was thinking about, but this is just spit-balling ideas was whether or not to have a "Shadow Controller" on the homeworld for the alt-response, make it essentially invincible but give it some kind of HP like attribute that grows as your champion does (eg, 1 knowledge = 1 point here) and the AI response can target this instead. If they reduce the points to zero there could be a number of consequences: your champion is disabled for x minutes or the champion loses a random upgrade as a couple of suggestions.
One thing on hacking, since the AI is after-all an all powerful computer network, would it not be appropriate for it to have some kind of response in kind to hacking? Now whether this would be on by default, an AI type, a counter hacker plot in the lobby I'm not sure, it would be up to the community to balance but I do think its a mechanic which would add some interesting results:
A Percentage chance to disable turrets, specific ships, shields, etc on waves. Temporarily disabling facilities, disrupting supply on planets. (Obviously the potential is as extensive as the options available to human hacking)