I was just there with DS5 and DS3. We stayed for a week and saw all the Disney parks. For my children, if I was going for 3 days I would go to Magic Kingdom twice and either Epcot or Animal Kingdom once depending on what your kids like.
MGM was fun and had good shows but if you ask my kids what they liked best it was the torrential downpour that we were caught out in! They loved playing in the rain. They did not want to go back to this park.
Animal Kingdom was good. It had a couple of kiddie rides. There weren't many animals out when we went on the safari. The Boneyard was fun. If your kids love animals/dinosaurs I would choose this.
Epcot they really enjoyed the Kidcot stations. They went from country to country and got their tokens. They loved Soarin' and the GM test track. If your kids like exciting rides and doing hands on stuff, I would choose this. Also if you want to eat a good meal on property Epcot would be my choice.
My kids loved the Magic Kingdom. We went back 3 times (one for
MNSSHP) and they still wanted more! This is the park with mostly kids in mind. There are more rides for them, good character interaction, and cool things to see. I would definately do this 2 times. Save the other parks for when they are a little older.
After all this, if you are like me, you'll say "but I want 3 different parks" so I would go with Epcot, Magic Kingdom and Animal Kingdom.