I don't think I've ever seen that episode. But I haven't watched a lot of the original Star Trek Series. Underground farming and mining would be a wonderful addition.
I thought about what a tube mono rail high speed transportation system above the existing tunnels might be like. I think it could look great and be fun to construct but it could be distracting to gameplay. If done right it may not be so bad given that you can change your view in the 3D interface.
I hope they give us better controls over exploring the colonies view. Only being able to toggle through views of the tube sections kinda sucks. I'd like to have a fly through zoom in and out control similar to the Sims 3 when you press "tab". It's great because you can also edit a text doc and adjust the speed and limits of zooming.
I just hope they release the next version soon! Looking forward to checking out the new features.