First...I'm certain you will love either no matter which you choose!
However, I have stayed at the Grand Floridian with my dd11 twice in the past and ended up at the Poly due to room availability one time. There are some big differences that I noticed...
-GF had bright and airy decor, Poly is darker (too dark for me) and it seemed dingy and a bit run down (which could have changed since the refurb). As a previous poster mentioned.
-Rooms seemed overall cleaner at the GF...could be due to the lighting and decor...or possibly our comfort level.
-GF is definately more centralized and we enjoyed the smaller size, Poly is quite spread out and it was a hike to the GCH (main bldg). I'm sure it just depends on your room location at the Poly.
-The Poly elevators looked like they were from the 70's..a very small dingy box (important as my dd11 and mother are both a little claustraphobic and HATED these elevators), GF elevators seemed brighter and roomier (if elevators matter at all)
-GF Main Bldg Lobby was very relaxing...and believe it or not we did stop and relax a few times. The Poly lobby is not very relaxing (for us)...other than the water feature it always seemed so hustle n bustle.
-GF Quick Service area seemed smaller but more organized. I like the arcade was right in the QS area as I could keep an eye on my daughter and relax with a snack. There is also the option to eat outside at umbrella tables and watch fireworks while overlooking the marina. The Poly Quick Service area was larger and more chaotic. The outside tables overlooked the garden area towards the pool.
...GF it was always sunny, Poly it rained all the time...OOOPS!!! Sorry, that is not due to the resort...just coincidence!!!
All in all...we prefer the GF over the Poly (my dd11 does too...she says it is like going home when we go to the GF).
Hope this helps!