Another vote for "don't drive" -- I'm not sure where you'll be flying in from, but if it involves an overnight flight (e.g. from US/Canada), you do NOT want to be going straight from your flight to the Autobahn and crazy German drivers at much higher speeds than you may be used to...

Or at least stay in Berlin a couple of nights before you go on to anywhere. Believe me, you do not want to be trying to change lanes between the right hand lane (trucks going 50-65mph) and left hand lane (Mercs and Beemers going 100-150mph) on the back of jetlag.

Once you've left Berlin... I hear Regensburg and Passau are nice. Nürnberg is also worth a stop.