You're going to have to make some painful decisions, I fear. I love art and architecture (especially Art Nouveau and Art Deco), and I spent about a month in the Netherlands and a month in Belgium last year. Pay attention to the location of the sights on your short list and try not to spend too much time traveling from one to the next.
For the Kroller-Muller museum, I wonder whether you might get by with just a single night there (if you can solve the luggage-storage issue). The museum is great, and the sculpture park is larger than I was expecting; I didn't do adequate research on the latter and ended up not having enough time outdoors. And I traveled there from Arnhem, which is closer than Amsterdam, so I might be wrong about the timing. Still, I'd suggest you take a look at the rail and bus schedules to see whether you could squeeze this stop to just one night. I say that because there is so much to see and do in Amsterdam as well as other Dutch cities. One other thing: Be sure you get on the right bus! I had to transfer, saw a bus waiting and jumped on it. It quickly became clear I was going in the wrong direction--another reason I didn't have enough time for the entire sculpture park.
For Belgium, Ghent is the most centrally located city for day trips to the others. However, you don't walk right into the historic center as you leave Gent Sint Pieters Station (extending the time it takes to reach other cities). In addition, I am not a fan of making multiple day trips to the same city--which you might need to do for Brussels. I don't think this is a clear-cut decision.
Brussels is a gold mine of Art Nouveau architecture. It is all over the place, and there are some lovely buildings whose interiors can be toured. I don't think you're going to have much time to chase that sort of thing, however. It happens that in Ghent there are some beautiful Art Nouveau exteriors very, very near the train station. Exit the station and walk to the right. It's worth doing even if encumbered by luggage. The historic center of Ghent has some very impressive guild halls as well. You'll probably want to hop on a bus or tram to get to the center from the train station.
Rick lists his top sightseeing tips for many major cities on this very website: Follow each of these links, click on the name of each city you expect to visit, then click on "At a Glance".
Top sights in Dutch cities
Top sights in Belgian cities
Part of Brussels' Royal Museum of Fine Arts has been closed for building work. The Magritte Museum and the Old Masters Museum are both accessible and worthwhile. Smaller art museums that might be of interest are the Bozar and Charlier Museums.
