"After Dark" DLC did add the day/night cycle. I think you could skip stops before that (running different lines through the same tubes, but going to different stations). I can't recall for sure.
Four metro stations. A, B, C, D. Stations B and C are placed on loop sidings so metro trains stopped at those stations do not block the main line. They only interfere with main line trains if they meet at a junction, and then only briefly (compared to waiting at the station).
The red line goes A-B-C-D and back.
The green line goes A-D and back, skipping stations B and C.
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Then you can take the example above, and instead of having both running at the same time (all day), then (see picture below) set one of the lines for day, and the other for night.
In my example, red line is "all stops", and day only (sun radio button) is selected. Stops at A-B-C-D.
The green line is "express", and night only (moon radio button) is selected. Stops at A-D.
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You can do whatever you want. Have one line go A-C and another go B-D. Or A-C-D.
Instead of A-B-C-D-C-B-A, you could also do A-B-C-D-A if you wanted.
Hope that makes sense.