My guess is the 2-year-old may enjoy the views of animals more at AKL.... but if you plan to spend time in the restaurants there, he might be happier with the food at WL. My DS10 didn't like the food at Boma when we stayed there (too exotic for him), but he could handle the snack bar place ok. On the other hand, he loved the Whispering Canyon restaurant, as well as the Roaring Forks snack bar at WL 2 years earlier when we were there.
Having said that, his highlight was seeing the animals at AKL, and they are EVERYWHERE. Not sure about a 2-year-old, but those are my thoughts.