Cities similar to Florence and Seville

I suspect my suggestions aren't practical given the big cities you are thinking of. But based on wonderful recent visits to Krakow and Gdansk, I think they might be worth considering, perhaps especially Krakow. Both have old/main towns of beautiful "old" buildings, castles in or nearby, churches, lots of museums (both older art, at least in Krakow, and 20th century history in both), they are very walkable and have a cafe-culture in various squares. Weather would be different to Sevilla, though. However, I'm not sure how transport would work from the other cities you mention; at a guess, there would be flights to Krakow at least from all three (?).

The other place that springs to mind is York. Not sure it has a cafe-culture as such, but it has Bettys, plus the history, walkability and big mix of top sights.

I would say that a smaller city in Spain that could fit your criteria would be Zaragoza, the capital of the Aragon region of northern Spain. The city has more than 2,000 years of history, from the Roman city walls and amphitheater; to the Aljafería, an 11th-century fortified Moorish palace. It's also the home of the famous pilgrimage site of Nuestra Señora del Pilar Basilica, housing the miraculous image of the Virgin Mary of Pilar.

Zaragoza also has some pretty good day trips close by, like the Royal Palace of Olite, one of the most impressive medieval palaces in Europe. It was the seat of the Kings of Navarre. Another interesting site is the Loarre Castle, one of the oldest castles in Spain, it was featured in Ridley Scott's epic film Kingdom of Heaven. The Loarre Castle is very picturesque as it sits high on a cliff overlooking the southern foothills of the Pyrenees.

Zaragoza remains relatively unknown and undiscovered compared to the rest of Spain. Hopefully this is along the lines of what you were thinking of :)

That's a really interesting question, and I share your love of smaller places.

Do you have a particular time of year for your trip? Amsterdam tends to be damp and cool (though I guess we don't know these days), whereas Prague can be quite hot in mid-summer. I had heat in Berlin in 2015, but I think overcast and not so hot is sometimes what you get.

I liked Gdansk and Krakow very much. In fact I spent a great five weeks just traveling around Poland this summer. The other major cities I visited were Warsaw (too large for this list, I guess), Poznan and Wroclaw. Poznan and Wroclaw are not quite as site-rich as Gdansk and Krakow, but they have things to see (probably more in Wroclaw--but it was German pre-WW II). I haven't checked rail routings, but Poland should work well with Berlin, logistically. There's also the really gorgeous much smaller city of Goerlitz sitting on the German-Polish border east of Dresden.

One thing that wouldn't stop me, but might give you pause, is that so many of the major museums/historical sights in Berlin, Krakow and Gdansk are related to 20th century historical events, especially WWII and the Cold War. I love that stuff, but there's not as much variety as you might get if you went in a different direction. One could enjoy Gdansk and Krakow a great deal without overdosing on what happened in the 20th century; Berlin doesn't have the same physical beauty, but does have tons of museums on art and a variety of subjects. Still, you mentioned "things to see", so I assume you want to do more than wander around and look at gorgeous facades.

I believe the Polish options would be workable if your major city was Prague, too.

Other possibilities: Dresden-Leipzig (with side-trip to Goerlitz, though I'd rather spend the night), Erfurt (with Weimar and Eisenach), Brno (with side-trip to Olomouc). Farther afield (cheap flight?): Zagreb, Ljubljana.

Florence and Seville are two of my favorite cities.

Here are some of my favorite European cities that are not large.

Brugges, Belgium
Trier, Germany
Heidelberg, Germany
Strassbourg, France
York, England
Porto, Portugal
Segovia, Spain
Krakow, Poland
Bergen, Norway
Salzburg, Austria

Edinburgh in Scotland.
Copenhagen.
Reykjavik.

Zaragoza and Girona would make for a pair of wonderful smaller cities just outside of Barcelona.

Maastricht, The Netherlands - old Roman city, bicycling the countryside, university, old world feel, Rainbow Spiral Hundertwasser
Leiden, The Netherlands - 17th century tulip mania, Pilgrim Fathers, canals, M.C. Escher
York, England - English history, York Minster, medieval town
Dresden, Germany - reconstructed glory, bier
Heraklion, Crete - ancient Knossos site and museum, vibrant night life, great food, varied occupation rulers
Arles, France - van Gogh sites, Camargue National Park, great food, wine, Roman ruins,
Colmar, France - great food, wine, museums, canals, medieval town, storks

The list is endless. Generally most of Europe is full of those types of cities. A couple I would add are
Ghant
Bruges
Haarlem
Delft
etc.,etc.

We have enjoyed these smaller cities:

UK: Bath and Edinburgh

Italy: Palermo

France: Chartres, Arles and Nice

Some smaller cities that I found easy to manage with plenty to see and do: York, Liverpool, Salzburg, Siena, Cordoba, Wurtzburg, Verona, Nimes, Arles, Copenhagen, Valladolid, Tallinn, Gdansk, Oslo, Stockholm.