First: A disclaimer. I have not played a game with the core shield generators. I don't think they'd effect my play style much - though I don't always get all the ARS's before I hit the first homeworld. But, I can understand the feeling of getting 'roped into' playing a certain way, which seems to be the perception around here.
Here's an alternate mechanic that I *think* accomplishes much the same thing as the core shield generators, but keeps player options there.
Instead of forcing the player to destroy shield generators, make it so that the AI homeworlds cannot be attacked until the AIP reaches a certain level - maybe 200-500 or whatever. You have the freedom to do whatever you want to get the AIP up to that level (just throw some nukes around if you want), but if you try to go onto an AI homeworld before the AIP hits that level, the AI either A: launches *really* nasty waves at you (maybe these are special waves, or maybe the AI just gets some MASSIVE but temporary effective AIP boost until you get off it's homeworlds) or B: has shields so you just can't hit the homeworlds period. An in-game justification for the former method is easy: the AI essentially panics because it thought it'd reduced the humans to nothing, but suddenly they're on its homeworld? Better send in the special forces to quell the rebellion... but after the AIP hits a certain point, the AI perceieves the human threat as 'nominal' so it doesn't do this. Or maybe the AI home planets are invulnerable because they have a delicate home shield grid reinforced through its gate network or something - increasing AIP usually means you're taking planets, so you're destroying gates. Hopefully someone else can think of something better - the mechanic is the interesting part :-)
Perhaps 2-3 (maybe more) AI "Threat Assessors" are seeded throughout the galaxy, which reduce the AIP needed to assail the homeworlds by some amount - so you still have the freedom to play a relatively low (or lower) AIP game if you want to. But you have to hold these things in order to reduce the AIP needed, and if the AI ambushes you and you lose control of the planet, you could find yourself facing some very nasty AI waves. or in the best case simply be unable to assail the AI homeworld until you recapture it. Oh, and in order to get the AIP reduction, the Threat Assessor needs an active link into the AI warpgate network (needs to be adjacent to an AI planet with a warpgate), so the planet with it WILL be threatened by the AI.
Optionally, it could be mandatory to take and hold one or more of these threat assessors to hit the homeworld.
Here's an example of how this might work:
You need 500 AIP before you can attack the AI homeworld. Each "Threat Assessor" reduces the AIP needed to hit a homeworld by 50 (could be anywhere between 50-100, depending on the number of these things we have). You want to hit the AI early, but not too early, so you take one of them. You now have to spread your forces out to defend the Threat Assessor while you hit the AI Homeworld.