We will be ending a Rhine cruise in September 2020 @ Basel. Flying home from Frankfurt. We are looking for a 2-3 itinerary by train. Ideal would be a train ride to a destination and travel out from there. Any ideas?
I suggest you consider the small towns in France--Eguisheim, Kayserberg, Riquewihr, Ribeauville, and more. You could base in Colmar. Sorry, don't know if that can be done by train. Have a great trip.
Strasbourg, Colmar, Belfort and Besançon France are destinations near Basel. Geneva and Lausanne are close by as well. Here are two towns close to Frankfurt along the rail line that you could visit on your way to Frankfurt.
Wiesbaden and Mainz Germany.
Basel is a lovely city with an interesting town center. Depending on your interests you could spend at least a full day there. Close to Basel are some Roman ruins you can get to with public transportation. Luzern is a spectacular town to visit and easily visited by train from Basel.
If you are looking for ideas close to Frankfurt, I don't have anything beyond the cities on the Rhine which I presume you will be visiting. Sometimes the Rhine cruises do offer excursions to the Alsace as well, if not those would be great places to visit, but except for Colmar, I feel very difficult to visit by public transportation. I've noticed lately that some of the Rhine tours are not visiting Heidelburg. I found Heidelburg very picturesque with an interesting castle.