Hi Elise,
You are choosing between two wonderful resorts. I can see why this is a tough decision!
Bay Lake Tower at Disney's Contemporary Resort is beautiful, sleek, and modern. The quick walk or monorail ride to Magic Kingdom is amazing! On the other hand, the immersive and fun theme at
Disney's Art of Animation Resort is wonderful. You truly feel like you have walked into a movie.
I think that how each family goes to the theme parks is very personal. My family likes to go to a theme park early in the morning and then come home in the early afternoon for a rest or swim in the pool. Later in the day, we may head back to a theme park, or to another resort for dinner. I know many families who like to go to a park and stay there all day long - from the time the park opens until after the fireworks at night. It really depends on your family. Do you think that your little ones will still need an afternoon break? Bear in mind that it does take a lot of energy to be in a theme park. Even if they have given up naps, they may still benefit from an afternoon break.
Of the two that you are considering, if you are going to spend the most time at Magic Kingdom and Epcot and use Disney transportation, Bay Lake Tower will be the quickest to get to and from. I really do enjoy the theme at Bay Lake Tower, and the pool is very nice and has a fun slide and water splash play area for children. That said, the colorful theme at Disney's Art of Animation Resort may appeal more to your children - especially the amazing pools.
I hope that these thoughts help you to make your decision, Elise. Have a great time planning, and please do not hesitate to ask if you have any further questions.