In the past I've found that players don't enjoy situations where "you get cool toy X, and the AI gets cool toy Y as a direct counter right in its face". Like when player golems used to trigger huge reinforcements on an AI planet they were on. Golems were very seldom used back then. That felt like a treadmill situation, and people seem to much prefer "get exos periodically thrown at my empire, in return for my having this big gun" to "the AI reinforces hugely as soon as I show up with this big gun".
I'm not 100% sure that would be the situation with champions, but I suspect it wouldn't be great.
What I am suggesting would be something that grows in proportion to time spent in AI territory and depth into AI territory, with a bonus for important systems. Spend 5-10 minutes in their territory next door to your world and they will politely request you get out. Try to deepstrike and shorten the response to 1 minute. The longer you ignore their polite requests to leave, the more forceful they make their requests, until the champions either have to leave, or will die. The response levels will drop quickly over time, but will not result in 0 response simply by destroying a command station.
My biggest beef is the challenge for destroying guardposts on a world with ONLY champions is very low compared to using fleet ships. The biggest challenge for a champion comes not from the threat fleet, but from special forces, which barring the existence of certain ships inside, the champions can "Benny Hill" or turtle their way through. Even if there are problematic ships in there, they can usually outrun the AI's special forces long enough to destroy all guard posts and command station, and be back in time to kill any AI response before they become an issue.
No, I think the AI's response should be more directed against stopping champions before the damage is dealt. A growing chance of response, and attempt to push them back out. I think the following dirty tricks should be added to make things more challenging in the normal game for champions:
Chance to replace reinforcement waves with ships that counter/harass champions well, chosen from currently unlocked ships. Will give examples below.
As above, but if selected ship type has been corrupted, attempt to spend budget on core versions. If it hasn't been corrupted instead make sure it spends it on at least the mark level of champion ships' highest level module.
(The above are reinforcements, and will not leave the planet and join the threat fleet unless normal conversion conditions apply)
AI makes specific purchases from the Trader to prevent champions from passing through/leaving etc. Only valid if trader is in system. Possibilities include sudden decision to place Black Hole Generators, Orbital Mass Drivers, Radar Jammers, and Super Fortresses. (This will discourage champions from attacking when the trader is in the area.)
Retaliation wave: Normal wave strength wave consisting of shadow vessels using normal wave destination logic, or directed at the system champions are located. Will be announced as normal, but successive waves during a span of time where the champions have not reentered friendly territory will have shorter and shorter timers. (20% for each wave)
Finally give the AI a chance to improve one of it's shadow vessels up to the next hull type, capping out at the player's shadow hull type. This is per champion the players bring with them.
Furthermore, I think that nebulas have been around long enough for the AI to take notice of them. I think it's high time the AI starts having some response to champions making contact with others isolated in said nebulas. The AI has shadow vessels right? (This should be restricted to games with 2 or more players however as it could be overwhelming for a single player) Also threat of this should end the moment a mission is won/lost. The AI never cries over spilled milk.
Responses will occur beginning and during missions in any nebulas connected directly to AI systems or their immediate borders. Responses will begin at closest command station with a warp gate, and attempt to fly into the nebula, and then immediately target the closest friendly base and try to destroy it. They will be announced with 30 seconds to 1 minute timers, will consist of half #of player champions in strength rounded down, be the same size as the player champions, and can be intercepted before they enter by normal fleets. However this is more and more unlikely the deeper into AI territory you go to get to a mission unless you somehow have a standing fleet there able to survive there. Note: This behavior either should be disabled for Core AI worlds/Homeworlds or logic should prevent nebulas from spawning on those worlds.
Doing this part will discourage champion players from simply deep-striking wherever they can to perform all their missions quickly and gain massive amounts of power that the AI cannot combat until very late in the game. Deep-striking now would provide severe risk that the players would not be able to finish a mission due to AI shadow reinforcements.
Here is a list of ship types that aggravate/annoy the heck out of champions:
Zombards
Sentinel Frigates
Bombers
Electric Bombers
Speed Boosters (in combination with other ships like Bombers)
Armor Rotters
Blade Spawners
Yng Tigers (not usually used in reinforcements, this is a special case)
Vampire Claws
Viral Shredders (really anything shield immune)
Raiders
Tackle Drone Launchers (Only with other ships and Only if drones are used by champions)
Gravity Rippers (and the other kind that slow down nearby ships)
Snipers
Plasma Siege Starships
Heavy Bomber Starships
Sniper guardians
Spider guardians
Enclave guardians
Disassembler guardians
Plasma guardians
Summary: Give the AI tools that it can use to oust these invaders effectively. Don't make them use the tools right away, instead make it more likely to use them the longer they stay in enemy territory or the deeper in their territory they go. Give them a cool down ramp so that champions can't just duck out or destroy a command station to reset the aggression level. Make the AI challenge a champion's ability to do wormhole missions in all but the safest locations, requiring assistance outside the wormhole to allow the mission to go without interference. This way you place limits on what champions can do against the AI without simply directly countering them at every move.