Short trip to Alsace or More Bavaria?

The Alsace to / from will cost you nearly a full day. Maybe other destinations are closer, e.g. Würzburg, Worms, Heidelberg or others. Bamberg is definitely worth a trip. If you like beer try a smoked beer.

If you will travel (partially) by rental car you can find a lot of scenic routes in Germany on the website of German National Tourist Board.

I assume that you plan to drive for the whole trip. BUT, 3.5 hours of driving is half a day, and you have a lot of driving already included. Great roads, but..... We break our trips up into AM and PM and Evening segments. Travel segments all mostly end up being half days because they include checking out of lodgings and checking into the new ones.

Rothenberg ob der Tauber (1 day is right, brilliant church, by the way) and Nuremberg (2 days will be very tight, particularly if travel is included and if you have any interest in the nazi story there rather than just castle/museums/churches) are in the opposite direction of Alsace. If you want Alsace then they are the outliers geographically here, and take three of your 15 days. And bring you down around Munich (on the highway!!!) to get to southern Bavaria.

"Alsace" is pretty general, so what do you want to do there/around there? Heidelberg in the Rhine Valley is very nice. Strasbourg is gorgeous and worth a day if not more. Baden-Wurtemburg includes the Black Forest region, Baden-Baden and Fribourg, which deserve more than a day or two.

If Alsace is important enough, then drop Rothenberg and Nuremberg for this trip and do a big counterclockwise circle: Rhine Valley, south to the Heidelberg/Strasbourg/Black Forest area, east to Fussen/Castles, and end in Munich. Or, if you really want R and N drive north from Munich to see them and back. Or, Nuremberg is 90 minutes by train from Munich so ditch the car and head up there for a day or two by rail.

If you want 3 days on the Rhine - not a bad idea at all if you want to do some walking, biking, or take a side trip somewhere - you should add a night there. Your first day after a long overnight international flight will likely men a lot of "down time" as you deal with possible flight delays, baggage + security + transit, jet-lag, drowsiness, and inner-clock adjustments. Suggest you avoid driving on Day 1 for these reasons.

Bamberg, Iphofen, Bad Windsheim, Würzburg, and a few other places are very much worth visiting. I'd allocate at least 2 more nights to the 3 nights you've set aside for Rothenburg and Nuremberg as well.

Alsace is of course somewhat different from the Rhine and Franconia (Nuremberg, Rothenburg etc,) but maybe not all that much - all are wine regions, with a degree affection for half-timbered buildings, and a strong regional cuisine.

Iphofen: http://tramino.s3.amazonaws.com/s/iphofen/685626/stadtplan-iphofen-english.pdf

Bad Windsheim: https://www.tripadvisor.com/Attraction_Review-g198421-d284746-Reviews-Frankonian_Open_Air_Museum-Bad_Windsheim_Middle_Franconia_Franconia_Bavaria.html

To clarify, we were thinking a full day in each Colmar and Strasbourg, and be based out of Colmar.