Another point, regarding turbolift shafts.
It's a good idea to have "passing zone" stops (without doors) along longer runs. Since these tubes are two-way, but only one-lane, you'll inevitably have places where you'll have two cars trying to pass each other and not be able to... and end up with traffic jams.
Yes, if you have an unoccupied "car docking station" (which you clearly HAVE considered) you can use those. But it's impossible to predict what's happening when, so it just makes sense to have a few "side stop" points where one car can move to the side and allow another one to slip past it, then slip back into the tube and move on.
Alternatively, you COULD try creating complete "loops" (each tube only goes one way!). In a Galaxy-size ship, that's actually pretty practical. But in a smaller vessel, it's damned hard, just to route (and it also takes up a lot more of the available space). So I think just adding a few "passing zones" would fix the problem more effectively.