Complex sentence: The Cologne Stadtbahn is not a true subway system; even though a large part of the system operates underground, especially in the downtown area, each line crosses at least one street at street level without absolute right of way.
Split into simpler sentences: The Cologne Stadtbahn is not a true subway system, while a large part of the system operates underground, especially in the downtown area. Still, each line crosses at least one street at street level without absolute right of way.