Hello! I have stayed at both Wilderness Lodge and Poly so hopefully I can give some insight. Wilderness Lodge was/ still is my favorite resort theming wise, and I always enjoy staying there. However, for my last trip I was given the opportunity to stay at the Polynesian. Being an avid fan of the WL I was hesitant, but I decided to go for the Poly, and I do have to say it was really worth it. Being on the monorail was both a time saver and a magical touch. The theming at the resort was fun, and I really enjoyed the vibe at the resort. Also there's nothing like looking across the lagoon to the Magic Kingdom. Overall my stay at the Poly was definitely one of the best trips I have taken because everything was a little extra special being in one of the original WDW hotels. While I am sure you would have a pleasant stay at the Wilderness Lodge, I think you should go with the Polynesian because the construction/ elevator issues may take away from the Wilderness Lodge experience right now. I recommend staying there some day, but you really can't go wrong with the Poly. If you're gonna spring for a deluxe, the Polynesian is definitely one of the best ones to do that at. You won't be disappointed.
Good luck with you're decision, let me know if you have any more questions.