So chokepoints are the most efficent method of defense.
Long term, maybe this can be looked at. I say long term, because I doubt any consensus will be developed on how to tackle this.
However, I present an idea to help reduce the mathmatical "range" which map types can present. This won't necessarily be pretty, but it will reduce the desire for those maps which naturally encourage chokepoints.
This method would also address another problem. Once a player makes a chokepoint, for the most part that is the player empire. By necessity, any worlds outside the chokepoint are outposts. The AIP costs of ruining another group of chokepoints (around 15 AIP) is simply not worthwhile.
The idea:
A player constucted unit which causes an increase of AIP of several warp gates, which causes all waves to attack the planet it is on. If the wave is "triggered" when the unit is on a planet that normally cannot be attacked, it does nothing. It would have a cap of one. This unit can be moved, slowly, allowing new chokepoints as a player empire grows. It has a cap of 1, and cannot be transported, but is [perma]-cloaked