It is made up of wooden cases with dirty glass and one label per 30 exhibits or so, beyond the label saying 7th Century cemetery of Ancient Thera. There's not much to say museologically. The cases need renewing, the building has problems with water entering and causing walls to pop and the iron inside the concrete to crack in certain places (and this on an island which is traditionally considered dry).
The exhibition itself contains a pretty interesting batch of finds from all the periods usually covered. There are some very nice Attic ceramics, some daedalic figurines from graveyards and the sanctuary of Aphrodite and some good kouros statues. There is plenty of potential for this museum to be spruced up nicely, but at the moment it remains a type-case example of the crap old-school approach to museums as warehouses of stored antiquities.