In the first scenario, Berlin, your stops are going to be massively overcrowded. Don't worry about it too much. Don't panic and buy lots of buses/trams for each line as they'll just get stuck in the traffic.
Buses: Be very aware of traffic, I try to keep them off the large roads that are going to get busy.
Trams: Try to build the tracks on the roads as little as possible. The 4 lane roads with grass in the middle are perfect for trams.
Metro: Massive money maker, but very expensive to build.
Loans: Don't be too afraid of taking out loans, especially when building the metro. Each metro train should pull in roughly 300-400 a month. So two or three trains should be more than enough to cover the repayment of a loan.