Suggestions: Frankfurt the town is meh, but the surrounding countryside is one of the best parts of Germany. Rent a car, and explore the small towns on the Rhine between Frankfurt and Koblenz. There are a ton of small castles along that river that have loads of character. Riverside cafes, ect. are pretty great in that part of the world as well. If you venture towards the French border, the terrain gets hillier, and is pretty awesome as well.
I recommend Marksburg Castle,Toll station Pfaltzgrafstein, Castles Katz and Maus along the Rhine. Boppard has Roman ruins, and is a great place to stay the night or to have a good meal and have as a stopover. Loreley rock is cool enough, I guess, and the view is pretty good. Koblenz itself is a beautiful town, and worth the trip as well. It's very old.
If you are heading in the direction of France, Triefels is a cool place to go. Honestly, there is a tonne of exploring you could do in this area. I been there 4 times, and I still have not seen the best of the area. My favorite part of Germany.
Dresden is awesome. Still has some Communist architecture and public art. They have done a good job at restoring the old town. Lots of fun.
Munich. a 40min car ride from Munich is the famous Neuschwanstein castle. The inspiration for Disney. Should be one of the wonders of the world.
Right up against the mountains. If you are going to Germany, this is a place you must go to. It's not far from Munich, and I think there are tour buses that you can use to get there if you do not want to drive a car.
Speaking of Driving, the Autobahn is a lot of fun in and of itself. You can go as fast as your car will let you. And you will be passed regardless of how fast you are going. Stay to the right, and watch out for cars flashing their lights behind you. That means they are coming up fast.
Munich is also the best place for beer gardens and drinking. Berlin has a better nightlife, and Munich has better beer gardens.
If you do go to Berlin, there is a ton of things to do there, as well. However, if you are expecting to see the wall, you're about 10 years too late. The Germans are doing their best to forget that they ever were communist, and that there is anything different between the east and the west. A piece of the wall is still standing, but it's pathetic. But don't let this dissuade you from going to Berlin. It's still a really fun city, everything there is changing very quickly.
I have gone 4 times in the last 15 years, and have spent a grand total of about 6-7 months in Germany. Sometimes it feels like it's the only part of the world I actually know. Not enough people go there, it's a great place to travel to.