I would really just like to see performance issues improved when your colony starts to get too big. Having too many building makes the game start to lag really hard. Also the game seems to have a real hard time loading the grey screen when previewing a building or tunnel you want to build if you are too close to a spot on the map you can not place the building. Main example being on Hyla's Crescent attempting to place buildings near the waters edge takes a long time for it to load and gets a little buggy trying to create a tunnel path. That and the more buildings you have, the longer it takes to load and place a new building each time.
A minor fix would also be the funny looking texture on the loading screen for the winter map with the river flowing down the mountain. It looks like it is flowing over a flat surface instead of falling down a mountain.
It would also be cool if you could do partial designs to the maps such as resource placements for the sandbox mode as well as the arrangement of the starting colony buildings and how they are connected.
Sandbox mode with the Referendums set to Never should also be able to access all of the various policies you can put into place.
Another idea might be an upgraded tunnel that allows quick transport of your citizens to various locations. The main reason behind this is because I love to zone and organize my colony into districts and it would be cool to me if I could put the housing in one area and the farming in another, etc. without having to intermingle them into a mess just so the citizens are close enough to where they work. Obviously the tunnels would be an upgrade that would cost more nanites to upgrade or build, and would consume more power. But the benefit would be that citizens do not feel that it takes too long to get to work.