My kids have been traveling to WDW every year since they were born. I think a lot depends on how YOU want to do the parks. For us, walkability was huge as it's a pain to deal with strollers on the buses (and this is coming from a city mom who was used to it). Fortunately both kids liked the front pack, which made it easier.
Assuming that you want this experience to be about your kids and not just dragging them to whatever you want to do, a lot will depend on their personalities. Eg. when DS was not quite 3 he rode Barnstormer 8 times in a row one day and was a champ at the parks. At 2 he loved swimming in the pool and having a bubble bath every night with the jets on. At 3, DD only wanted to do character meet and greets and even at 4 was pretty terrified of everything. My niece just went at 4 and only managed to do carousel and the Frozen singalong successfully. She was dragged on Small World and Peter Pan, lost her mind, and was done for the trip. She did spend 6+ hours/day in the pools though and every time she talks to my mom she asks to go back to Disney.
Does that mean that you shouldn't take little kids? ABSOLUTELY NOT, especially as a
DVC family. DD actually learned how to read by texting Disney words to my mom, and even after many MANY trips each trip somehow manages to be better than the last.
So getting back to your original question...
If your kids are going to be big in the parks, MK and AK are probably going to be preferable to Epcot and HS based on the rides that are there. In that case I would probably bite the bullet and stay at a walkable MK hotel, as that will make your life easier. DS loved eating under the monorail as a toddler, but the pools at BLT are not that great. VGF and Poly weren't walkable when my kids were little, though they are now. CC is a fantastic resort with nice pools and a wonderfully relaxing location by the water, but the transportation situation isn't as favorable if you are trying to get into the parks easily.
If your kids are going to be happier in the water, it's really hard to beat BC, though Poly is a good alternative for a MK resort.
If your kids love animals, aren't going to be in the parks that much, or you are willing to drive AKV have a lot going on for them. The pool at Kidani is great for little kids and there's a lot to see for non-Disney families.
In case your kids end up having a tough time, for DD one saving grace was the idea of an "anytime snack bag," which we actually tethered to the stroller and let her eat out of any time she wanted. We also bought her a "brave blanket" - a large muslin that we could use to cover her stroller - after the disastrous 3 year old trip. Just knowing it was available to her was very helpful. Finally, we had a pixie dust experience where a CM bought her an "invisibility wand" that would turn her invisible in front of storm troopers in HS after they saw she was having a hard time. She went from having to LEAVE the park one day because we saw Darth Vader hundreds of feet away to having a storm trooper walk right past her stroller with no reaction. I will always remember that little bit of kindness that they showed her that day.
