My brother installed the game on my computer because it wouldn't run well on his. I've played a couple games, after the very brief tutorial and run into the same problems every time. Regardless of how I try bypass tracks I always get trains stuck going in and out of cities. With four tracks in and out and all sorts of chances to hop from one track to the next you think the trains would be able to sort out a system to get in and out? But no. So I started playing on the easy setting for train movement.
Unfortunately you *can't* hope for the trains to "look ahead" and pick the best route - that is, in fact, one of the game's main challenges.
While it could've been tweaked to be more forgiving for beginners (actually, I'd say "medium" difficulty a good forgiving setting), you have to remember that each train essentially needs its own rail line.
It sucks, but it's the most efficient way to lay out your tracks.
Take a look at how the the AI routes its tracks; with some exceptions, it's generally a good example.
The only place where you'll end up trains "switching/sharing" tracks is at large terminals, where you only have 4 tracks available. If you only have three trains coming in, each should have its own track. Terminals can have 4; beyond that, tread carefully - 5 or 6 can work, much more than that and you're probably going to get gridlock
One hack, of course, is to buy out a competitor and use *his* stations.
Then I ran into the little issue of train jumpers. A couple times on a more complex route my train got lost and started jumping around. I'd go from an annex to a city and take the manufactured goods somewhere while heading back to the annex but instead of heading the right direction at some point it makes a wrong turn and then starts jumping about 1/2 a screen on the tracks and being stuck in a perpetual loop of going nowhere. I've played flash games for longer than I've enjoyed this one, I'm just glad I didn't pay money for it.
Nasty/stupid bug - delete the train or completely re-route it; excessively complex tracks may contribute to it, unfortunately.