[...] Also for some reason I didn't complete the mission asking me to move 50 passengers via that tram, even though I clearly was connected to the 3 hubs (university, train station, theater) that it asked for.
You can't complete mission by using hubs. If the mission asks you to cover train station, university and theater, a single line should do the job. If a mission asks you to go from airport to a house in the opposite side of the map, only 1 line should do it. Don't get the wrong message, lines should be short, at least bus and tram lines. The missions are not a good way to learn how to play. Unfortunately, in those cases you will need to build the line just to get the money and then demolish. Those lines are not profitable.
I'm about to fire it up and give it another go. I'll try more, shorter bus lines.
Yes, try shorter lines.
Berlin is a special case. You will find other maps easier to play.
Do you see in downtown some avenues? Try making tram lines there, then you avoid traffic. The avenues in downtown will let you connect train station and the other train station with a lot of offices without having too much trouble with traffic.