For 2 days in Germany at the end of May, Berlin or Munich (or somewhere in between)?

Two or three days is not enough for Berlin or Bavaria so I would spend it on the Rhine River. Bacharach is a 1h 45m train ride from the FRA airport that requires a transfer in Mainz. I would sleep there to explore the Rhine.

I agree with MaryPat. A couple days along the Rhine would be a lovely way to ease into your trip and shake off any jet lag. We like to stay in Boppard, but Bacharach is as cute a town as you could ask for. Take the train from Boppard, stop at St. Goar to see the fortress, then continue to Bacharach by train. Explore the town, then take the boat back to Boppard.

You might want to spend some time in Frankfurt, it has way more to see than what is in the Rick Steves book. (sorry, Rick) It is old, it is historic, and only Berlin has more museums. I have about 1000 posts on this forum describing the many things you can see and do here.

There are so many gorgeous towns nearby too, that I personally would love to spend a weekend in. Limburg, Marburg, Eltville, Idstein, Michelstadt, Seligenstadt, Mainz, Büdingen, Gelnhausen, Kronberg, Bad Homburg. All within an hour's train ride from Frankfurt.

The Rhein is an easy day trip from Frankfurt if you want to go there.
If you only have those 2 days, why spend them traveling? For one, you will be tired from your flight, jet lag can ruin a sightseeing day. Fly in and out of Frankfurt, and then you won't have any stress and be more relaxed once you get to Turkey.

Berlin is my favorite city.

EVER.

But

I agree with Ms. Jo.

Frankfurt and environs has a lot to offer.

I would hang out in/around Frankfurt for the intervening days.

And arrive well-rested in Istanbul.

Videos about Frankfurt kindly made by a resident of the city: https://www.youtube.com/channel/UCmjB2brbPgR16-rUTqFcGAg/videos

Thank you all for your wonderful suggestions. We are definitely rethinking our agenda and will most likely stay around Frankfurt or along the Rhine River. We might even plan our return trip through Frankfurt so that we can do both.

That would be a good decision.

Joining a walk through the city of Frankfurt is a great way to see it.

The travel section of Stars & Stripes newspaper has a number of articles on things to do around Frankfurt, for example, museums, Elvis, & the Taunus Mountains.

We are definitely rethinking our agenda and will most likely stay
around Frankfurt or along the Rhine River.

The Rhine Cruise starting in Bingen, as suggested by travel4fun, makes for a very fine introduction to the Rhine Valley. I suggest you do that right after arrival at FRA on the 25th, on your way to Rhine base town. The most scenic segment lies [between Bingen and St. Goar.]1 Board in Bingen and cruise to either St. Goar (1.5 hrs.) or Boppard (2.3 hrs.) Either town serves for a good base for a short stay. The train ride from FRA's Regionalbahnhof station to Bingen's Rhein-Stadt station (where the dock is close by) takes about 1 hr.

KD Cruises is the most prominent day cruise provider with the most departures. The 2022 cruise schedule w/pricing isn't out yet. In normal years there are 5 KD boats per day out of Bingen at 9:30, 10:30, 11:30, 14:30 and 16:30; pricing from a couple years ago was about €21 to St. Goar and €30 to Boppard. A 20% discount can be had if you show the TRAIN ticket you used to get to Bingen.

Outings from your base town:

From St. Goar (home of Rheinfels Castle) Bacharach is about 10 train minutes to the south; just 5 minutes to the south is handsome Oberwesel as well. Boppard is 10 minutes north. Marksburg Castle in Braubach is a must-see, intact medieval castle; Use the St. Goar ferry crossing (runs all day long) then walk north to the train station for the 20-minute ride to Braubach.

From Boppard use southbound trains to visit St. Goar, Oberwesel and Bacharach; use a northbound train to Koblenz and change trains there for a visit to Marksburg in Braubach.

Map of the area showing railways, ferry crossings; click on town names for more information:

http://www.loreley-info.com/eng/rhein-rhine/walking-hiking.php

How about figuring out your best connection to Istanbul before deciding on your Germany stay? I've visited both Berlin and Munich and you can't go wrong with either. With only a couple of days I'd probably just stay in Frankfurt and enjoy what it has to offer.