Cologne - yes or no.

I loved the four nights I spent in Cologne, several good museums in the city, great restaurants, and a river cruise is also possible. Aachen or Trier are other possibilities.

Saxenhausen Memorial is near Berlin.

"As an architect I do look forward to touring the Cologne Cathedral but, other than this site, I'm not sure a 3 day stopover in Cologne is a good use of my time. I am open to day trips outside the city of Cologne but not sure where to go. (I am considering Bonn and/or Frankfort.)"

Unless Cologne's museums appeal to you I'd keep my time in Cologne short.

"While in Germany I would also like to visit a concentration camp..."

You can visit the Cologne cathedral and Cologne's Nazi Documentation Center (housed in a former Gestapo building) in fairly short order. It's not a gruesome "camp" but a memorial site.

http://www.museenkoeln.de/ns-dokumentationszentrum/pages/315.aspx?s=315

"...is there a better city to visit by train between Bruges and Berlin for these 3 nights?"

IMO it would be an act of negligence not to spend a couple of days visiting the old-world, half-timbered towns and medieval castles in the Middle Rhine Valley, a UNESCO World Heritage site. Bacharach, Oberwesel, St. Goar, Boppard and Braubach would all be handsome towns to stay in and good bases - from your base travel up/down the river valley by local train to visit the other towns, Marksburg Castle in Braubach and Rheinfels in St. Goar. Then there's Burg Eltz in the nearby Mosel Valley (train + hike in.)

After 2 days in this area, spend a day and a night in Cologne on the way to Berlin.

Berlin has a lot of new, unique architecture, so not sure what style appeals to you the most. I would plan on more than 3 nights there. Maybe do a day trip to Potsdam which has those lovely, old palaces.

If you would like to visit a Concentration Camp, there are 2 that are near Berlin. Sachsenhausen and Ravensbruck. Ravensbruck was for women. Both have excellent exhibits, museums and many original buildings which can be very chilling when you enter.

Frankfurt isn't in your line of travel though there is very wide variety of great architecture here, from Carolingen, to Gothic, Half-Timbered, to Industrial Revolution with a few Art Deco buildings in there mixed in with skyscrapers. The Deutsche Architecture Museum is here if that is of interest.
http://www.dam-online.de/portal/en/Start/Start/0/0/0/0/1841.aspx

Cologne - yes or no.

Yes, one of my favorite German big cities. There is more there than a cathedral.

I would definitely allow time to take a Rhine River Cruise. Cologne is a great jumping off location for going south on the Rhine. There are a lot of great towns that you can explore from the river cruise.

That's what we did. Few days in Cologne and trips to Bonn (excellent History Museum), Düsseldorf (possibly must see for an architect) and Frankfurt. Great time.

I had to go to Cologne earlier this year. It was "interesting" but not a place I would ever go out of my way to visit. It was sort of dirty when I was there. To be fair, it was the dead of winter; maybe nicer in the spring.

As an architect, you may want to spend more time in Berlin. Here is a video of the architecture in Berlin after the Fall of the Wall - a fascinating blend of historic and modern with interviews of David Chipperfield and Daniel Liebeskind.
http://www.dw.com/en/arts21-urban-experiment-berlin-architecture-after-the-fall-of-the-wall/av-36272279

I can't imagine dedicating the same amount of nights to Bruges and to Paris, nor spending more time in Bruges than in Berlin! Perhaps you planned to make some daytrips from there, perhaps to see the newest Zaha Hadid in Antwerp, or architecture (or historic architecture there and in Brussels.) Because you mentioned the excellent cities of Dresden and Leipzig (note spelling), I don't think you have used Google Maps to think about actual distances. Mentioning Stonehenge, which is a terrible idea for a first four days in London, is another clue that you have unrealistic plans for transportation. You also failed to say whether you plan to use public transportation entirely, or if you will rent a car.

While Bruges is not far from Brussels, Brussels (or Antwerp) are right on the way from Paris to Cologne. Bruges is not "right" on the way. Belgian local trains are cheap and frequent, and don't require reservations. It is also much easier to make day trips there than in Paris, only because Paris has so many train stations, for going to different regions of the country.

I recommend that you add you home city to your profile, and tell us if you have ever been to Europe before. You will get better advice that way.

I would recommend that an architect stay in Brussels or, better, Antwerp, and daytrip to Bruges. Note that there are medieval buildings in all three of those cities. I happen to like Cologne very much, but I agree that if you don't like museums (an architect would want to see the Kolumba and the Applied Arts museums, as well as the Dom. The newer Ethnographic museum would be a design site, as well as the Philharmonic, the modern art museum, and the Romansich museum.

Dresden and Leipzig are closer together than either is to Berlin. I wouldn't want to make separate day-trips to those two cities from Berlin, and I doubt that you'd be happy seeing them on the same day. However, I'm not an architect and don't know your approach to sightseeing.

You have more on your plate than you'll have time for, but I can't resist mentioning one of my favorite stops on my 2015 trip: Görlitz. It's on the Polish border, about an hour from Dresden by train. The city escaped the war basically unscathed and has been nicely restored. There are over 1000 half-timbered buildings, accompanied by some Jugendstil edifices scattered about. I think it would be a real treat for an architect. You could base yourself in Dresden and see both Leipzig and Görlitz from there (not on the same day).

Alternatively, the stunning town of Quedlinburg is about a 75-minute drive from Leipzig (longer by train). It also has nearly uncountable medieval buildings as well as some Jugendstil. There's a castle, an art museum (Feininger), and an important church treasury with an American connection.

"As an architect I do look forward to touring the Cologne Cathedral but, other than this site, I'm not sure a 3 day stopover in Cologne is a good use of my time. I am open to day trips outside the city of Cologne but not sure where to go."
I think two days in Cologne will be enough. For the evening I would recommend a beer tasting tour in the old town - "Kölsch" is a kind of beer you only get in Cologne (and Bonn).
Besides the Cologne Cathedral there are twelve romanesque churches in Cologne of which at least four or five are definitely worth visiting.
And for the third day I would also recommend a side trip to Aachen.