DEFINITELY combine Bruges and Ghent. It's a 22 to 28 minute direct train trip that runs 4-6 times an hour in the daytime. You waste time changing hotels, and it feels so much better to be in the same room for 4 night than two different rooms for 2 nights.
I'd stay in Ghent. It has 80 percent the pretty historic buildings as Bruges, but is more of a real city and less of a touristy Disney type of place. Ghent has a university, a thriving restaurant scene, a fantastic castle with creepy dungeons, different city districts. Bruges is at the end of the line for the train (almost) while Ghent is more central if you want to go elsewhere.
If weather cooperates, the bike ride from Bruges to Ghent, or in reverse, is a lot of fun. Use the train one way - easy to do. Or ride there and back. You follow a paved canal-side bike road almost the entire way. Rental of regular or e-bike is simple.
I like Delft, have stayed there twice in the past five summers. We have friends who live close by, so have toured around with locals. The Best Western recommended above is a fine hotel. But I would argue that you can "do" Delft easily in an afternoon/evening no problem by getting off the train and storing your bags. It's a short train trip from Ghent, and even shorter from Amsterdam.
I also strongly feel that Den Bosch is the Netherlands best small city between Flanders to Amsterdam. Den Bosch is relatively unknown to international tourists, who are much more likely to know of and go to Delft. Den Bosch is full of Dutch, Belgian and other European holiday makers. It's a very interesting, good looking, and lively city with what the Dutch call a "Burgundian" lifestyle. It has a surprising cafe culture for being in a cool and rainy part of Europe. If I was staying a night or two I'd likely go to Den Bosch. Passing through for a long afternoon then charming little Delft.
From Ghent and Amsterdam you can easily day trip to all the destinations you list above. These are little countries with fast and efficient rail systems. It would not be inconvenient to stay 4 of your 9 night is Ghent (day trip to Bruges and Antwerp) and 5 remaining night in Amsterdam (and day trip to Utrecht and Leiden). In fact this itinerary would likely be the most enjoyable and relaxing. Or stay in Utrecht instead of Amsterdam if you prefer a less intense less big city experience. In a flash you are in Amsterdam from Utrecht. There's a lot to see and do in Amsterdam though, so if you have a long Amsterdam must list then staying there is the best call.
Have fun! The Low Countries are just wonderful :)
