That's due to the federal states and their different interests and rivalries. Something like Jüterbog halfway between Berlin and very populated Leipzig/Halle area next to the railway line would have been perfect and almost ready to use. There are, even today, huge deserted former soviet military tank firing ranges available for redevelopment. But this would have been the next Frankfurt airport and national hub that none of the old players wanted.
Combined with local narrow minded state politicians they ended up with the - too close to the city - BER site.