I think they are roughly about the same size, but with a studio at the BCV you also get a microwave and mini kitchen area which might be beneficial with the children. I think you need to ask yourself which location will be more convenient for you and where your interests lie. If you think your toddler will be thrilled with seeing animals up close, and you like the theming of AKL, and don't mind that it isn't within walking distance of anything, then choose that resort, especially if you are looking for a more laid back, quiet trip.
On the other hand, if the mini kitchen, proximity to Epcot/MGM/Boardwalk, Stormalong Bay pool, appeal to you, then choose the BCV studio. I love both resorts for very different reasons. If I were you I'd be choosing the BCV studio just for the convenience though.