Just to give you a perspective (and a comparison to BER), the project began in 1992. The planning permit process began in late 1993 (and wasn't entirely finalized until 2012). Construction began in 1996, was stopped in 1999 due to political issues, resumed in 2003 and is now finally done.
In other words, it took over 20 years to build 70 miles of track and I guarantee you the terrain wasn't the main factor in that. That's just the reality of infrastructure projects in Germany today.