Hi Brandi,
This is such a great question. I do find that there is not an easy answer, it depends on the preferences of your family. I am going to highlight the must do activities for each Theme Park to make it easier for you to make your decision.
Disney's Animal Kingdom is a great Theme Park for families who LOVE animals. The Kilimanjaro Safari is absolutely amazing! Your children will also be able to experience some fabulous attractions such as TriceraTop Spin, the Boneyard, Festival of the Lion King, Finding Nemo - The Musical, Wildlife Express Train, Affection Section, Conservation Station, Discovery Island Trails, it's Tough to be a bug, Flights of Wonder, Maharajah Jungle Trek, Mickey's Jammin' Jungle Parade and Kali River Rapids if you are adventurous.
Disney's Hollywood Studios offers very different attractions and experiences, based around popular movies. Some of the popular attractions for younger children would be Toy Story Mania!, Disney Junior - Live on Stage!, Beauty and the Beast - Live on Stage, MuppetVision 3-D, Voyage of the Little Mermaid, "Honey I Shrunk the Kids" Movie Set Adventure, and Star Tours again of your children are among the brave.
From experience, I find that my four year old has more fun at Disney's Hollywood Studios, because it is different from any Theme Park we we have at home. Disney's Animal Kingdom is beautiful, however it is very similar to visiting the zoo that is close to our home. It is best to look at your options and decide which Theme Park will work best for your family. If you have any other questions, please let me know. I would be happy to help.
Stephanie