Hi Erika!
Hmmmm, so, deciding whether to do 2 days at Animal Kingdom or 2 days at Hollywood Studios? Using my family as a barometer (children ages 7 and 3), we can almost always get through Hollywood Studios in 1 day if we start in the morning.
Animal Kingdom, however, if we took our time, could be stretched over 2 days. There's definitely much more to do there with children your age, and 3 and 5 is generally that age where kids love animals. So I can envision them spending a lot of time in the Affection Section, where they can pet the animals, the Boneyard, where the can dig for bones, or even the Discovery Island Trails, where they can see more animals.
So, I would go for 2 at Animal Kingdom and 1 at Hollywood Studios.
Have a most excellent time!