While reading this topic i had a stroke of brilliance. Her it goes.
I am a big fan of Xcom series and since the new big DLC is a few month away i have been putting some serious hours in that game. In Xcom you get adjacency bonuses for placing structures of one type next to one another put 2 labs to one another and you get a research speed bonus, put 2 workshops together and you get manufacturing discount on construction completion, satellite up links give bonus satellite slots and so on.
I think this system has allot of potential within galciv.
Lets make a few examples.
First of all it would be great if you yourself could place the initial colony structure where ever you desire, this can be a straight out feature or unlockable with tech or both. To avoid abuse i think initial colony structure should be restricted to bare tiles (no bonus tiles). Or again ability to place it on bonus tiles could be unlocked with research.
That said Colony structure is building responsible for all social and scientific production and if you build factories next to it you will receive social production bonuses or if you build labs you get sci. prod. bonus. Bonuses can be ether flat production, or maby a cut for construction time fx. 1 week cut for every 2 factories up to a maximum of 3, this is where hex system could come in because you can only build up to a 6 building around central hex.
Now since initial colony structure is responsible for soc. and sci. prod. the star port will be the head structure for the mil. prod. so if you build plants next to it you wil get similar bonuses as mentioned above to mil. prod.
I always found galcivII planet building system exciting(compared to SM CivIII) but a bit flat in the long run since after you have filled bonus tiles you could just place the rest of the buildings in absolutely random spots with no bonus or penalty.
Since there are many different buildings in the game with many different bonuses and traits you can come up with a myriad of adjacency bonuses. I think my suggestions can really create a very big pool of possibilities for adding depth to the planet building portion of the game.
I rly hope someone will read this because i my brain was spitting like crazy her 
P.S. sry for any grammar mistakes.