Brussels has a few bad neighbourhoods too. Maybe have a quick look around the Grand Place and some surrounding streets, and leave the city that has been disappointing everybody since the 1500's.
Bruges is gorgeous but it's also like Venice in the sense that there is a level of tourism that makes it into an attraction rather than a living, buzzing city. Ghent is somewhat similar on historic beauty but is much bigger and less touristy. Antwerp's bloom era is a bit younger but otherwise comparable to Ghent. I personally like cities being cities more. The Belgian coast is not really interesting, it's all seaside appartement blocks, Dutch coast line is protected against that so much more beautiful and natural. But you'll notice the difference in Belgian and Dutch building regulations in more than one way. One of the great things about Flanders is that are chance of something amusingly absurd round the corner anywhere.
I agree with some posters above about The Hague, and it has a beach. Cycling through the dunes there and is popular, appearently people enjoy to have both the headwind and the hills. I'm Dutch and therefore it's hard to be impressed with cities like Delft, Gouda and Leiden, but they are interesting, and they are all different but not that much. I'd skip Gouda, the cheese named after it is made elsewhere too and pick either one of the other two. Both have a huge history. A bit of a hidden gem is Dordrecht, the "most Italian city of the Netherlands". Historically hugely important too but it had it's hayday before the others, 15th and 16th century rather than 17th century, which has shaped most of the Netherlands.
Agree about the Utrechtste Vecht too (I always start reading topics only to find it's very old after I've finished) but in general Flanders and especially the West of the Netherlands are shaped by waterways and that's where there is a lot of nice cycling next to it. Many cycle paths started out centuries ago for the horse drawn boats, whcih was the public transport of the 16th and 17th century. . .