Lets see if anyone else has been thinking about this. I'm going to assume that they will be returning in GC3, but I wonder what improvements they will be making to them. The change I think needs to be made is that they need to be put in their own section of the build menu. Mostly so we can tell what ones are galactic wonders and what ones are just buildings.
Something I want to see added is more steps to building a wonder. Right now you just build or simply buy them. (Who thought it was a good idea to buy them.) I'd like to see requirements like you need to find 3 sources of focusing lasers, one level 5 captain and build barracks before you can build the Tir-quan training base. You could start without everything, but your progress would be gated along the way till you find the required remorse for that step. I am thinking that these extra steps could add some more depth and planing to building a GW. It helps tie wonders into other systems like Exploring, diplomacy, combat, and it even ties it closer into building and planet management.
I think that the wonders would have more exotic powers. Some are neat, some are kind of flat. Most (really all) should be some level of exciting past just a bonus to this or that stat. Tir-quan training base could unlock a new invasion ability in addition to it's soldering bonus.
My final thought is why can we only have one wonder? It seems like more of a gameplay thing to allow the different fractions to evolve differently and form out abilities only they have well also encouraging a form of economic combat as only one side can finish that wonder. I think there might be better ways to accomplish these better goals through different mechanics.