Brussels/ Bruges and Berlin

"Bruges needs at least two nights and a full, well-organized day." (Rick Steves, Best of Europe)
He doesn't even include Brussels in his Best of Europe book.

Brussels is in between Berlin and Bruges, although of course Bruges is way closer to Brussels than Berlin. So this means your trip is going to go involve a little back-tracking, no matter what order you do it in.

I know a lot of people will say to stay in Bruges at least 1 night (and maybe 2) so you get an evening and a morning without the crowds, and a lot of people don't particularly like Brussels. If you're phobic about crowds, then maybe that's a good idea.

I stayed in Brussels for 3 nights and took 2 day trips - one to Bruges for the whole day, and one to Gent and Antwerp for 1/2 day each. Trains between the cities are cheap and fast (about an hour or less between each of them). I didn't find the crowds in Bruges too overwhelming and I found that 1 day was enough to do what I wanted to do. I went pretty early so I was there when most of the attractions opened up (I was in the first group to climb the bell tower, which was a good idea based on the lines later in the day). I followed the RS suggestions for 1 day and did everything except the brewery tour. As for Brussels itself, I found that I saw as much as I wanted to of Brussels in the evenings and early mornings - I'm not a big museum person so it was mostly just walking around absorbing the atmosphere, enjoying breakfast or dinner at a cafe, and people watching.

As you noted the best flights would be into one city and out of the other but I don't think it's important which order you do them in. Look at airfares and see if there are differences. When I planned my trip I found that it was about $200 less to fly into Brussels and home from Budapest, rather than the other way around, and the timing of the flights was better that way too.

I spent 5 nights in Berlin and felt it was a good amount of time for a first visit. I liked Berlin a lot and would love to go back for more. So, in my opinion, I would spend 5 nights in Berlin and 3 in Brussels (or 2 in Bruges and 1 in Brussels - the night before you fly out).

Getting between the two would be either a long train ride or a pretty short flight, depending on which you prefer. The train is about 7 hours (city center to city center) and the flight is about 1-1/2 hr (actual flight time, you have to include getting to and from airports and check in and waiting for flight). I'm a train person and will always choose that over flying if possible. If you're ambitious travelers you can break up the train journey in another city for a couple of hours, which is probably what I would do. For instance, Brussels to Cologne is <2 hrs, spend a couple of hours in Cologne seeing the cathedral and having lunch, then Cologne to Berlin is about 4-1/2 hours.

There's no need to spend a night in Brussels, as it's only an hour from Bruges, with trains twice an hour connecting them. And the trains are unreserved, so you don't even need to plan ahead; whenever you're ready to leave Brussels, you can just take the next train back to Bruges.

To find flights between Brussels airport and Berlin, use Skyscanner: http://www.skyscanner.com/. Be aware that Brussels Airport (code BRU) is much easier to reach from Bruges than Brussels Charleroi Airport (code CRL). Berlin has two airports, and you probably don't have a reason to favor one; so, use the code BER to pull up "all Berlin airports." Looking at a random date in May, I see a number of nonstops from BRU, with prices starting at $66.

To find trains, use the Bahn (German Rail) website http://reiseauskunft.bahn.de/bin/query.exe/en following Rick's tutorial: http://www.ricksteves.com/travel-tips/transportation/trains/online-schedules. Your starting station is Bruges(B), and your ending station is Berlin Hbf. A quick look shows that the fastest routes are 8 hours with two changes. Some of the tickets can be bought in advance on that website at a discount, if you can live with tickets that have restrictions on refunds and exchanges.

As for which city to do first, I'd see which direction works out cheapest. For no clear reason, it may be much cheaper to go US to Berlin and Brussels to the US than the other way. Or, the one-way airfare between your two cities may be much lower in one direction on the day you want to go.

How many nights in each? That, of course depends on your goals. But Berlin is MUCH larger than Bruges. You could easily spend all 8 days in Berlin and not run out of "first tier" things to do, while Bruges's designated "sights" will only take 2 days or so. That doesn't mean Bruges isn't a nice place to relax, particularly in the evenings. And if you feel "done" with Bruges, you can take easy day trips to Antwerp or Ghent as well as Brussels.

The same thinking may influence which city you want to see first. Do you want to start in the small one to get acclimated, or leave the small one for later, to relax after the big city?

EDIT: cross posting with Nancy - I see great minds think alike.

I used rome2rio.com Brussels Airlines has multiple flights daily from BRU to TXL (Tegel Berlin). Flights are about 1.5 hours, so even factoring in all the extra time needed for flying (to/from airport, check-in, security, luggage collection) it's still shorter than the 6.75 hours on the train from Brussels to Berlin.

I recommend staying in Belgium in Ghent (which I like more than Bruges). It's about halfway between Bruges and Brussels, so convenient for day trips to both, has its own sights and charms and lodging is cheaper.

All in all, I'd just fly round-trip to Berlin and stay there the whole time. You can take a day trip to Potsdam, even one to Dresden, though I'd recommend spending at least 1 and, even better, 2 nights. . . even if you arrive late and depart early, using only one day there. Dresden is lovely after dark. Both are very different from Berlin. You can also go directly from Dresden to or from the airport, making it only one hotel change.

I stayed in Brugge, Gent, Brussels and Antwerp, and I loved them all. I agree with Chani that Gent is better located to daytrip in each direction.