Absolutely. Berlin is one of the more expensive cities in Germany. I can't speak for Leipzig because I don't know about the "intellectual atmosphere" OP is talking about. Just know that Göttingen is a good example because I have a friend that lives there.
Leipzig is way cheaper. I hear people comparing Leipzig to Berlin as of ten years ago or so when it comes to cost.
And 10 years from now we'll be talking about.. I dunno, Offenburg? Within Germany places like Leipzig and Tubingen seem very appealing (though I quite fancied a 600 year old house in Rothenburg Ob der Tauber - car free towns are lovely)