Just as there are upgraded amenities when you switch from a value resort to a moderate, there are greater increases when you go from a moderate to a deluxe. The deluxe resorts really give the best Disney has to offer. Spending a few nights at a value and a few at a deluxe is a way that many guests balance out costs while getting a taste of the good life.
My family's favorite deluxe resort is the Beach Club. You can read about this
HERE and
HERE. But it sounds like you want to be in the Magic Kingdom area. If you're deciding between the Wilderness Lodge and the Polynesian, there is really no wrong choice. These are both wonderful resorts with great service, well-appointed rooms, beautiful pools, and magnificent landscaping.
Personally, I prefer the the themeing at the Wilderness Lodge. This resort has my favorite feel at WDW, I love the woody atmosphere, architecture and decor. I even purchased several lamps for my own home after seeing something similar at the WL. Also, both Artist Point and the Whispering Canyon Cafe are on my list of top ten restaurants at WDW.
On the other hand, the Poly has probably the best transportation situation in all of WDW. You can hop on the monorail from there for the quick trip to the MK. The Poly is also a quick walk to the Transportation and Ticket Center which has other transport options to the rest of WDW, including the monorail to Epcot. If you have small kids, that monorail convenience could be a big deciding factor.
Good luck deciding and again, you really can't go wrong.