Not your average museum
This is true. It's a real charmer as these things go, and a great location halfway between the tourist market and the harbour.
The museum benefits greatly from being (nearly) all in one lovely high-ceilinged room (see attached photo), with beautiful painted larnakes (late minoan clay coffins) and mosaics running down the centre aisle. It somehow seems more manageable this way, although there's plenty to see.
As noted, the outdoor lapidarium area is shady, green and peaceful, and plays host to a clowder of well-fed local kitties and seats you can admire them from.
If you've made the hike along the E4 to Lissos near Sougia, check out the statue of Aesclepius recovered from his magnificent temple there (on the left, past the large case with the bull-statues), as well as a beautiful bust of his daughter Hygeia (on the opposite side of the aisle). Also cool is the Master Seal, which shows what appears to a view of Minoan Chania (Kydonia) from the sea (just inside the entrance gate, on the left).
As satisfying a museum visit as you're likely to have anywhere, and open quite late by Cretan standards (i.e. it doesn't close at 3 like everywhere else).