Both resorts are great. There is a significant price difference between them. If the cost is in your budget, I would go with the polynesian. It is on the monorail line, has larger rooms, has a view of the castle and fireworks from the beach and has direct monorail access to both the MK and Epcot.
The WL is also great. It is not on the monorail, but does have boat access to the MK, CR and FW. At the WL everything is under one roof so you do not have to go outside to get from your room to a restaurant, for example. For a luxury resort, the WL is a great value.
theming at both resorts is great. Both resorts are also slated to have some refurbishments ongoing during your visit, but it isn't expected to be something that should interfere with your enjoyment of your stay. At the WL book a courtyard view room to minimize the impact. At the Polynesian, book a lagoon view or Theme park view to reduce impact of construction issues. In both cases request rooms that are not near any construction.
Good luck!!