If I don't make moderate AIP (say, the 100 to 200 range) hurt really bad (at least on the higher difficulties), then many of you never get challenged, because you never go higher than that.
Basically the game has trained you "never ever take AIP unless you absolutely need to" and you have learned that lesson well Such that I then have to "chase" by bringing the serious AIP consequences down to where you keep it or the game's going to be a cakewalk (unless you have some non-AIP-based threat enabled like hybrids or FS, which can pose moderate to serious problems of their own).
Actually I think that's it right there. By moving away from AIP as the ONLY way to determine AI response, you can get some flexibilty in controlling the AI's actions.
For example, if the AI responds to destruction of the CSGs with significantly increased waves/CPAs/whatever, regardless of the AIP level, then you'd really want to take more planets to prepare for the AI's response. Sure, the AIP from those additional captured systems would hurt a bit through bigger waves and stuff, but if it is overshadowed by the response due to the CSGs going down, then it becomes worth it.
Another, similar, idea would be to have the AI response increase as the humans approach the AI homeworlds. If your closest system is 8 hops away, the AI-distance response is low. If you capture a Core world, the AI bumps up the response a LOT, even if the core world is only the second world captured.
A general ratio of human ships to AI ships is another potential response factor, or a total-human-firepower measure.
Now, some of these can be implemented through the current AIP scheme. Make taking down a CSG network give AIP +10/20/50/100/150 as each network goes down. Then rebalance so the AIP response is designed for 500 or so. Maybe add an 'invincibility' timer to the CSGs, so you are required to delay between destroying them (to prevent that last-second rush).
Distance to homeworld could be done by just adding more +AIP things (warp gates?) to worlds closer to the AI HWs.
I'm sure there are more, better ideas out there. But if there are ways OTHER than AIP to balance the AI, I think the players would be far more likely to take AIP.
The more I think on it, the more I'd be okay with removing the option to disable AIP auto-progress totally. I think it can be set to 1 per 60 minutes? That would have no (to very minor) effect on AIP throughout the game but the fact that it is on at all would change how the player plays.
I usually play with AIP/time on, using the default 1/30 mins. However, if I'm playing with Civ Leaders or Colony Rebellions, I don't. Those already require AIP/time response. Why require doubling up on that?