A few different thoughts at once gave me the idea for this total dick move of a plot.
So, the AI is trying to wipe you out. That's its goal in this part of the galaxy. It's got other objectives too, surely it's fighting other wars at the same time, so it's committing the minimum required to get the job done in human space. That's why humans can win: the AI underestimates them until it's suddenly too late.
When humans put up a big fight, the AI shouldn't keep underestimating them. AI forces warp into a system and get totally annihilated? That should be cause for alarm. If the AI thinks it should be able to pass through a few human worlds on the way to its target, then getting stopped cold at the first line of defense should be disturbing.
To that end: some kind of disincentive to vastly overpowering the AI. When you use ships of too high a mark, the AI gets its jimmies rustled: deploy mark IV ships against mark I waves and it freaks out and boosts AIP to compensate. Don't let it meet a quota of damage done per attack, and its waves grow unnaturally large until it breaks through. Wipe out its threatfleet too often and it gets very concerned, and starts guarding the fleet with extra Special Forces in its own territory. Instead of a whipping boy planet, you might need a sacrificial planet, a command center that the AI can destroy...because if you resist for too long with no planets lost, the AI starts thinking about sending a warhead to get the job done.
Some of this is partially covered by Red Queen level AIP progression, but there's more intent behind it. I feel like the AI needs more personality, and you should actually need to trick it... not just on a tactical or strategic level, but more trickery on the same cross-galactic theater that AIP exists in. The punishment doesn't have to be AIP, just an honest assessment of how threatening the player really is, and most importantly an assessment that the humans can trick by hiding their strongest resources. On a planetary level, take Threatening Eyes and go a little farther: if a subcommander loses a planet in an even fight, that's fine, but if it feels like the player is unnaturally overwhelming, it sends a message to the core world that the player might not be what they seem. Just think about what it would be like if your Mk.I and Mk.II ships were valuable because they look so weak.
I guess it would be a pretty big game-changer on the same level as hybrids. And it would be insanely difficult with the Shark plots...in fact, in a way it's the exact opposite of Shark. Instead of the AI picking up speed when it's successful, it picks up speed when it's not.
Just tossing it out there.
