This is a seriously tough question to answer! We have fallen in love with so many WDW resorts because of each of their unique theming; it is difficult to say that one is better than another. Perhaps I could point out some differences to help you decide:
WL has smaller rooms: 340 sq. feet compared to 409/448 sq. feet
WL uses only boats and buses for transportation - no monorail access
WL is one building; it makes getting around easier, especially during rain
WL doesn't have a view of the Magic Kingdom fireworks
WL has a lobby that beckons guests to sit and relax
WL has a jacuzzi; the Poly doesn't
WL is basically for parties of 4 while the Poly allows parties of 5
For us, the theming of the WL pool is better
WL doesn't have turn down service
WL offers families a chance to be the Flag Family of the Day (incredible views!)
WL has separate sinks/toilet-shower areas; not all rooms at the Poly have this
WL has balconies/patios while not all Poly rooms have balconies
WL has 2 sinks while not all Poly rooms have that
Since we are a family of 5, we haven't stayed in the Wilderness Lodge in the past 5 years; I truly miss the resort and wouldn't hesitate to stay there again!