Get extreme colonization! If that was your answer, then I guess you're weird like me.
But no, I'm serious. I don't know how that would do on the highest difficulty setting but on crippling or below it works just fine. I guess it has something to do with the way I play, which is to use super-breeder and torian technology (central mines for the win), politics of federalism with +30% econ boost, +50% military production, and +20% morale boost from custom points, get early star federation, and spam colonies like bacterium in a hot juicy vat.
But the logic is this:
1. Instead of wasting time and energy defending your colonies, just build more colony pods. You might lose 2 or 3 colonies due to AI attack, but if you can colonize 5 or 6 more you're still ahead. The point of the matter in this game is that it's really really hard invading colonies that are already set up, especially if they have a high population with central harvesters or farms on them already.
2. Instead of getting military techs, go the extreme habitat route. See point #1.
3. If you don't have starships, the AI's starships can't actually do anything. Congratulations AI you have this giant fleet. Unfortunately, since I don't have any starships, your fleet can't do anything and it'll still cost you 4-5 transports to invade one of my 50+ worlds. While you're busy doing that, I'll just go and expand to two other extreme colonies over there.
4. This game is about econ, econ, and more econ. The fighting and warring as I see it is almost secondary. Costs too much money and time! I mean, you have to research ships. Then you have to research weapons. Then you need planetary invasion. Ugh. With all those research points you could instead get extreme colonization, radioactive, toxic, water, and barren world colonization.
Be a corrupt corporate executive route and spread influence and spam colonies! Much more profitable and much less likely to get you embroiled in some giant unprofitable galactic war or something.