After some time spent on playing CIM2, I have found that you can actually make cims' pathfinding rational and efficient. There are however few compromises you have to make, however in my opinion they are worth it.
1. This is a master rule, without it the other points I'll make will not work. You have to ADJUST THE VEHICLE QUALITY IN THE RULESET TO ABOUT 300% (the point is, the quality of each vehicle must be 100%). The reason for this is that cims take into account the quality of vehicles when making pathfinding decisions. This is why masses of citizens get off metro and go to the tram just to go back to the same line of metro again, because the tram is more comfortable and they want to take few stops with it. In real life however, the quality of vehicles is not as important as the speed of getting from A to B. The changing of quality of vehicles will not make any substantial changes in the game (maybe it will make public transport more attractive). It will however change cims' priority to: METRO>TRAM>BUS. I tried it several times, it usually works.
2. CAREFULLY PLACE YOUR STOPS. The point here is that you want your CIMS to change in convenient terminals, or interchange stops, not run around few junctions to change from one line to another all the time. To do so, you need to place your local stops (not interchange stops) in a way, so that they don't overlap with other stops. Note that the ranges of the stops (circles) can overlap with each other. The center of one circle however shouldn't be within the range of another if you don't want CIMS to interchange. I'll show it on an example:
A) Stops overlap, interchanges will be made:

B) Stops don't overlap, interchanges will not be made:

C) Example of a terminal, stops overlap on purpose.

On this diagram I've made is the idea of two parallel lines which meet in the terminal point. (sorry for my poor paint skills :]) Note that if you place stops in the manner I suggest, CIMS will not be running between local stops and interchange only in the terminal.
3. DON'T USE SHARED LINES (in other words try to avoid situations where two lines occupy the same route). I know it's not like this in the real life, but unfortunately cims are not able to always get into the first bus/tram which comes to the stop if both vehicles are going in the same direction, they choose one line and wait for it. Also, if two lines are on the same route, cims will get off and on all the time and change lines going into the same direction, which doesn't make sense. So my rule is: one road, one line which meets with other lines only in interchange points which I have chosen. (see point 2)
4. DON'T MAKE WEEKEND/NIGHT ONLY LINES. This is very sad, but CIM2 engine doesn't allow us to make such lines, because CIM's will still want to get into the bus which doesn't operate on this day/time of day, they'll get mad and go on foot. I hope there will be a patch which will eventually fix this.
I hope those suggestions will help you get more fun from CIM2, despite its faults, as I did. Tell me if it works with your cities.
1. This is a master rule, without it the other points I'll make will not work. You have to ADJUST THE VEHICLE QUALITY IN THE RULESET TO ABOUT 300% (the point is, the quality of each vehicle must be 100%). The reason for this is that cims take into account the quality of vehicles when making pathfinding decisions. This is why masses of citizens get off metro and go to the tram just to go back to the same line of metro again, because the tram is more comfortable and they want to take few stops with it. In real life however, the quality of vehicles is not as important as the speed of getting from A to B. The changing of quality of vehicles will not make any substantial changes in the game (maybe it will make public transport more attractive). It will however change cims' priority to: METRO>TRAM>BUS. I tried it several times, it usually works.
2. CAREFULLY PLACE YOUR STOPS. The point here is that you want your CIMS to change in convenient terminals, or interchange stops, not run around few junctions to change from one line to another all the time. To do so, you need to place your local stops (not interchange stops) in a way, so that they don't overlap with other stops. Note that the ranges of the stops (circles) can overlap with each other. The center of one circle however shouldn't be within the range of another if you don't want CIMS to interchange. I'll show it on an example:
A) Stops overlap, interchanges will be made:

B) Stops don't overlap, interchanges will not be made:

C) Example of a terminal, stops overlap on purpose.

On this diagram I've made is the idea of two parallel lines which meet in the terminal point. (sorry for my poor paint skills :]) Note that if you place stops in the manner I suggest, CIMS will not be running between local stops and interchange only in the terminal.

3. DON'T USE SHARED LINES (in other words try to avoid situations where two lines occupy the same route). I know it's not like this in the real life, but unfortunately cims are not able to always get into the first bus/tram which comes to the stop if both vehicles are going in the same direction, they choose one line and wait for it. Also, if two lines are on the same route, cims will get off and on all the time and change lines going into the same direction, which doesn't make sense. So my rule is: one road, one line which meets with other lines only in interchange points which I have chosen. (see point 2)
4. DON'T MAKE WEEKEND/NIGHT ONLY LINES. This is very sad, but CIM2 engine doesn't allow us to make such lines, because CIM's will still want to get into the bus which doesn't operate on this day/time of day, they'll get mad and go on foot. I hope there will be a patch which will eventually fix this.
I hope those suggestions will help you get more fun from CIM2, despite its faults, as I did. Tell me if it works with your cities.
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