Looking for a suggested itinerary for Germany in late fall. We will probably fly into Frankfort and leave from Berlin. We are not adverse to renting a car either.
If you can, fly into Munich. It's more efficient to start your trip from there as Frankfort is more a place to fly thru (for most people) than an actual destination. Munich also has many interesting tourist sights within a couple of hours including the incredibly beautiful Austrian Alps of Western Tirol.
Wherever you land, the northern part of Bavaria - Franken - has a lot to offer: Würzburg, Nürnberg, Regensburg and Bamberg, just to mention a few. With a car at hand, the pilgrim church of Vierzehnheiligen (near Bad Staffelstein, north of Bamberg) is a less obvious, but recommendable stop.
Further on, Erfurt and the nearby towns like half-forgotten Gotha and a little bit touristy Weimar are worthwhile places to visit.
From here it's either Dresden or Leipzig.
And if you decide to fly into Munich instead, I can think of no better place to work off the jetlag on your first night than Therme Erding, conveniently located a 15 minute cab ride from the airport.
Adding to what the previous poster wrote... Bad Staffelstein is on the way to Coburg, which in my opinion, has Germany's best castle, the massive Veste Coburg.
The Region around Frankfurt has many interesting towns and the city itself is far more historical than many people give it credit for. It has a long, rich, Jewish culture, it was the site of the coronations and elections, as well as the 1st parliament. The Berlin Airlift happened here as well as the currency reform. (both times!)
Lots of wine festivals happening here in the fall, the Rhine is near-by and some of the quaintest towns are close to Frankfurt. Towns like Limburg, Marburg, Gelnhausen, Büdingen or Idstein. Mainz was the seat of the most powerful Archbishop and the cathedral is massive and 1000 years old. The Taunus mountains are beautiful and you can visit a Roman fort, Hessen Park Open air museum, and castles that have never been destroyed - Ronneburg or Kronberg, and the palace of Kaiser Wilhelm is in Bad Homburg.
Berlin is a quick 4 hour train ride away. Buy your tickets ahead of time and they will only cost 29 € p.p.
No, you don't have to fly into Munich, and yes, Non-Bavaria, i.e. the rest of the country, offers just as much as the Americanized sector of Germany.
Here is a map of Germanys highlights according to Baedeker, Germanys most popular travel guide:
Highlights of Germany
As you can see, plenty of things to see between Frankfurt and Berlin. On the direct route is what Rick Steves calls "Luther land", with the historically most important German castle, Luthers home, the Bauhaus and Bachs city. If you follow a more northern route you cross the Harz mountains, which offer a plethora of perfectly preserved half-timbered towns, among them several World Heritage Sites, and on a more southern/eastern route you can visit Saxony, a state with a combination of everything from large cities to small towns, wine and beer, castles and palaces, nature and traditions.
Your post is extremely vague. I don't know how anyone can respond with anything helpful.
How many nights IN Germany? Late Fall? In September or October? Early or late in which month? Maybe early November?
What interests you? Cities? Old towns? Countryside? Castles?
Alpine scenery? Museums? Hiking? Biking?
How many are traveling with you? Any children?
You're flying into Frankfurt, out of Berlin...good choice since you have a tight time constraint. I would do likewise.
After landing in Frankfurt, you can skip Bavaria entirely this time and head north and east into Germany, focusing on that part of Germany for these eleven days. . Flying out of Berlin certainly helps. Stay the first two nights in Frankfurt, then head to Hamburg, direct on the ICE. Visit Hamburg and Lübeck or Lüneburg for 3-4 days, then take the ICE direct Hamburg to Berlin. Spend the rest of the days in Berlin, doing a day trip or two...Potsdam, Weimar, Leipzig, Halle, . Late fall, ie October? In Berlin that means normally no more summer clothes, starts to get a bit brisk by then in Berlin. No need to rent a car for Berlin, unless you have the small villages in that area as part of your itinerary.
Be prepared. The trains are freaking expensive. If you are doing lot's of big city hopping the flex DB pass might be a good option.
Make sure you don't try to do too much. Every pretty, small town in germany starts looking the same if you try doing too many.
Every town basically has an impressive church, a charming/lively historic town square with overpriced restaurants, and some museums. Don't try to do a bunch of these in a row, spend several days in a bigger city and do a couple small town stops and really enjoy them.
The good news is: Except for frankfurt you really can't go wrong. I have been in cologne for over a week and have been enjoying it very much, even though I was expecting to have visited many other places at this point.
What type of stuff do you like?
Does hiking in the alps sound good?
Are you a history buff interested in the endless amount of museums, historical sights, and impressive cathedrals?
Which sounds more fun: Sitting in a traditional beer hall in Munich or staying up all night in a techno club, searching for a trendy, indie punk club in berlin?
Does the romantic rhine with hours of slow boat riding and wine tasting sound boring or relaxing to you?
Germany is really dense with great cities, history, and outdoor beauty so think about what sounds more fun for your trip.
Realize you won't get to do everything.
I have never thought of German trains as expensive. American trains...now THAT'S expensive. I have to repeat what Jo & Fred have said. Save plenty of time for Berlin - so much there. We loved Mainz - home to some surprising treasures. Schwerin is a great stop in the north. So many choices in Germany - no need to rent a car the trains are the best way to travel.