1) having different stations is not dumb, because say coal is usually not being loaded adjacent to passengers waiting for their express train. you can place a small goods station directly next to a passenger station however and just imagine that they are two parts of the same station. especially with modded stations or the planned modular stations it will be possible to create large railyards that consist of different parts but look like one large station. it does not have any effect on gameplay whatsoever if it is technically considered one station or not.
2) you can create a line that goes A -B -A -B – C – B – A i presume.
3) if you mean that cars should be able to be dropped and shunted around between different trains, yes thats sad that it is not oncluded. but it would also mean a incredible amount of programming work to make such a thing possible and it would be far to complicated for the average player. i would love such a feature but i think it goes far out of the scope of the game.
if you expect the train to magically add wagons out of thin air at a station and for them to disappear again at another station, then i am very thankful that such a feature does not exist in train fever. if you wan to transport different goods with the same train, you can add different kinds of wagons to the same train and transport different goods in one go.