Train lines: 2 or more stations?

Well, I think it highly depends on the line usage. If you have many people who want to travel from A to B, but only few, who want to travel from B to C, you'll probably make more money with two separate lines.
If the line usage on both parts is nearly the same, you should use a longer line from A to C via B, because the waiting time while changing lines adds to the total travel time. Which means people will travel to more distant houses when using longer lines (20 min time limit) and therefore generate more income.

Note that offering lines affects passengers. You cannot extrapolate from two lines usage what the combined one line would be doing in terms of additional traffic (unless you know all simulated inhabitants).

Also, I presume that passengers do not change vehicles unlimited even though they would not reach the travel limit of 20 minutes. It's hard to prove because you'd have to watch one single passenger traveling from start to destination and count the number of changes they do. Undoubtedly they at least use three vehicles in a row: Bus/tram to train station, the train itself, and bus/tram from the train station. I have personally witnessed passengers changing from one train to another, but I haven't watched them from the start to the end, so it may be they walked to the train station, travelling with two trains and a bus, and honoring such a 3-vehicle limit (which still is completely made up by me without facts).

However, if the number of lines used is limited (be it 3 or 4 or 5), then it would be beneficial to offer single lines that reach more destinations, i.e. not only simple A-B connections. And even if the number is not limited, each change of vehicles adds waiting time to the duration of travel.

Also, it is beneficial to not only use one station per city in the mid and late game. Have a station next to residential areas to allow passenger to quickly get to the station heading to the next cities, and have a station next to industrial to allow passengers to quickly get to their workplaces and back. Have train lines connecting one cities residential with another cities industrial area. Have bus/tram service connect the stations with commercial/leisure areas (these will be traveled less often IIRC).