So how about expanding that hyerspace gate idea a bit further; make it so you can "link" the gates on two barren planets (both from uninhabited) systems that would allow rapid travel between them. Just make the gate a structure you can build on them with a constructor module or something. Then whenever you have 2 gates created, link them up. Limit each gate to 1 other gate. You would still have to travel there to set it up. If one end gets blown up, both are gone.

There are plenty of existing techs to tag the planet gate onto.

Then you can reinforce remote sections of your empire in a gigantic galaxy in a few turns. Providing you can find a suitable area to build both gates in. Why would a superior tech race "fly" everywhere in bog standard warp fashion when not limited by the size of a ship?

I think it would provide a great dynamic to the game play! Even in smaller maps.

An option I think would be really fun is the ability to "detonate" a gas giant in a completely uninhabitable system, like in 2010. That star system would then become binary, and some of the planets could get a random PQ boost due to the extra solar energy. Of course, this would have to be far towards the upper end of the tech tree, as it would require something like a nanite swarm or super-advanced black monoliths (again, 2010) to convert enough of the planet's atmosphere to hydrogen to sustain fusion.