We just got back from Brugge and Brussel. We stayed at the Thon in Brussel and the Biskajer in Brugge. Thon was a basic, new hotel, but it had AC and we were on the 25th floor so the view was fantastic. Biskajer had a great breakfast included.
Mort Subite's beer was disappointing, but the building was really cool. If your time is limited, I'd stay away from Poechenellekelder too. It had a good selection, but the prices were high. It's right across from the Manneken Pis so most of the people there were buying cokes and didn't care about beer. Moeder Lambic was awesome. We went to the one on Fontainas. The staff was great and the selection was smaller, but better.
De Kelk in Brugge was awesome as well, with a huge selection and the bartender (owner?) really knew his stuff. There's a De Struise bottle shop in Brugge as well that's cool. Also Casa Patata had awesome fries and half chickens. That was really the best food we found. There are lots of places that are really expensive and not very good. Brussel has a lot more options for good food.
I would probably do like 2 days in Brugge and the rest of the time in Brussel. It's probably not as bad in the fall, but it was like Disney Land in Brugge. I think we saw maybe 5 locals in two days, and they were all at De Kelk.