Thank you for the article. The world is too big and time and money too short to see it all!
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In specifically german cuisine Id say mostly in sweets- walnuts, hazelnuts, almonds.There are plenty of non-fruit desserts as well but given the wide use of particularly almonds in pastries and cream elements its important to ask. Nuts may turn up in salads and other preparations as well. worth knowing the german names for the nuts to stay on the lookout (apart from traditional dishes, menu items will frequently list the major ingredients). I dont think it will be any harder to navigate a nut allergy in germany than in any other country in Europe, maybe less given the carefulness of menu descriptions there.
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Out of those 4, I’d choose Cologne.
If I was to choose 1 city for a one time visit to Germany, I would choose Berlin.
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Yes, beware possible nut oils in dressings, too. It’s probably worth printing out some allergy cards you can show the server and they potentially can bring to show BOH.
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Yes, Berlin for all the WWII and coldwar history.
Id just say you might want to consider Munich. Its at the other end of Germany but has a lovely laid back culture, beautiful river setting and top flight museums along with those bavarian foods and beers. Other towns and sights including the alps, the Romantic Road and even Salzburg within close reach. With Cologne, the Rhine and Mosel are near too. It all depends on what you are looking for and where else you are going.
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Stuttgart.
The problem is that there are too many Bavarians…
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Why? To be an outlier or because it has its own merits?
It’s the gateway to the East.
The museums are excellent.
The contemporary art is excellent.
It’s a beautiful city.
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Because that’s the only city I’ve been to on your list.
That said I do love Stuttgart. I probably go at least once every 2 years.
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Not a lot of nut-heavy dishes, but yea, predominantly in desserts. Plus as @honkman mentioned, most (if not all) menus will have an allergen list on the menu in both German and English.
Also, most Germans have a pretty good handle on English, so don’t be afraid to ask.
I think flying into Frankfurt gives you the most options. It’s not a long drive to Cologne from there, and neither is Stuttgart.
I don’t understand how anyone could love Stuttgart, the city proper.
Besides a few older buildings it is an overpriced, characterless eyesore. You have been warned.
PS: As a former / occasional resident of Berlin I appreciate the many recommendations to include it in your “touring” schedule, but the city deserves its own, dedicated trip. It’s a big city with LOTS of history — not just WWII btw — and it takes a few days to take it all in. Not to mention the manifold culinary & cultural offerings.
Happy to show you around if/when you come back 
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Cologne was the destination for my very first visit to Europe a million years ago.
I fell in love with the city…from the Dom to the lively riverfront, and 30 years later it’s still one of my favorite cities.
Everyone I met seemed to be personally invested to be sure that I liked their city…probably the warmest, friendliest welcome I’ve ever encountered.
Bonn is a short train ride away, and has the spun-sugar architecture that I love so well, plus a more small-city feel.
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The Rhineland has a reputation of being one of the most tolerant, open-minded & welcoming regions.
It has been referred to as the Ireland of Germany. We’re a friendly tribe 
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Having only toured two of the four, I’d pick Cologne over Stuttgart. Stuttgart seemed like shopping and not much else. Cologne has fascinating history. I’ve only been through Frankfurt for flights, I think, but it’s regarded more as a financial hub than tourist attraction.
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I have to agree. I spent a day there, once, and that was enough.
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tastes can differ - I havent travelled in Northern Germany (yet) though I grew up in Ohio with a ton of people with heritage from there. The Bavarians and Austrians seems to have achieved a pleasant work/life balance - they work hard but also can relax and their dining scene reflects it.
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I could easily spend a week and Stuttgart and not be bored.
Well, in fact, I have. Many times.
