This is my dilemma too. We are tentatively planning a trip for early next year. We will have me, DH, DMIL, and 2 DS's (3.5 and almost 2). I am torn between the Poly and Yacht Club.
I've made a pros and cons list, so maybe this will help you decide too:
YACHT CLUB:
PROS
-SAB pool has a sand bottom zero entry section IN the pool...kids can play in the wet sand and make sandcastles WITHOUT worrying about the bacteria in the lake water at Poly
(my oldest son is autistic, and he won't necessarily understand WHY he cannot go in the seven seas lagoon, even if I tell him he cannot---this could make him pretty upset)
-We love Epcot/not much interest in MK since we visit
Disneyland about every 2 weeks. For the record, I believe Epcot has just as much to interest kids as MK does. A large majority of the attractions at MK have height restrictions, while most at Epcot do NOT.
-Yacht Club has a workout room (crucial to DH, pretty important to me as well)
-Yacht Club is located all in one building (important when you have kids in strollers and it's raining)
-YC is a quiet, peaceful resort. Poly is very busy and loud in the main lobby, especially. YC has a very low key vibe, which is necessary to escape the mayhem of the parks
-location, location, location---lots of good dining/entertainment options just steps away
CONS:
-No real counter service options (although this can be remedied by utilizing room service, concierge, OR just buying some groceries to keep on hand)
-smaller room size...kids junk takes up a LOT of space, and the Poly wins out on room size
Now, onto the Polynesian:
PROS:
-on the monorail
-bigger rooms
-good pool, although I hear VERY often that it is overcrowded, which could be a problem
-location, location, location---lots of good restaurants to choose from on the monorail line, monorail to MK and close to TTC
-nicer grounds
-more kids activities during the day (although, they are probably more for older kids, as my kids would not get much out of learning how to make a lei or something, especially the 2 year old)
-GREAT restaurants on property. 2 of my favorites, Kona Cafe and 'Ohana are right there, plus the Tambu Lounge is AWESOME!!!
CONS:
-separate buildings (I really hate this in a hotel...just not my preference)
-OLDER buildings. I constantly hear of issues with mold/mildew smell, poor bathroom ventilation, broken a/c units, etc.
-longhouse location could be great or horrible, depending on where you end up and there's no way to guarantee in advance
-bus transport from Poly to AK, Downtown Disney, and MGM is pretty awful. I speak from firsthand experience catching buses from there several times
-it's more expensive, and harder to score on a discount there
-no hot tub in the pool
-no fitness facility on site (and YES, I do have a problem with walking to the GF one...I did that when I got a massage at the GF Spa and then had to walk over to the Poly for dinner. It's a long walk just to get to a workout room. Poly should have one onsite).
Overall, it's almost a pretty even tie for us. I think it will come down to which one we can get a better deal on. The Epcot resorts seem to have much more availability as far as discounts go because they are less popular overall than the MK resorts.
As for the transportation to the other parks, I think we will rent a car no matter what to get to the parks that require buses and to restaurants in other resorts, because after my last trip, I am just FED UP with the WDW bus system. You waste SO much time getting from point A to B that it really cuts into your vacation, and time is money! Renting a car for a week is so cheap these days that it doesn't make sense NOT to. Plus, with two restless toddlers, 2 strollers, and a huge backpack, riding the buses does not sound like my idea of fun. They know what a carseat is, they know how to behave when in one, etc. It's so easy to get around WDW property that I think if we have a car, we will be VERY glad we do, especially for going to Downtown Disney and to dinners/breakfasts that happen outside of park operating hours. Try and catch a bus from one resort back to your resort when the park near the restaurant closed an hour ago...now imagine doing it with a tired/cranky toddler...just rent a car!