My advice to you, don't OVER plan. I have seen families to busy checking their itinerary and rushing to the next 'scheduled' thing that they forget to RELAX. Be on vacation. It's Disney World. They end up missing all of the little things that make Disney a magical place.
If there are places you KNOW you want to eat at, make a priority seating. (Most places keep some time spots open for walk ups, so you can still get a PS for the same day, unless of course... Character Breakfasts and such.)
I don't know your party mix, so I will just give my general opinion.
Epcot - more adult, but still has some things for young children. Can be an all day thing, half day if you just want to do Future World and skip the World Showplace (which can take quite a while to simply walk around).
Magic Kingdom - all day event. Has something for everyone.
Animal Kingdom - half day. I have been to AK several times and have never ever ever spent a whole day here, there is simply not a whole lot to see since everything is spaced out. But I would recommed going, definitely see the Safari, Tough to be a Bug, and Dinosaur. If you have younger children, you can go to Camp Minnie/Mickey.
MGM - usually a whole day event if you want to see all of the shows. Not a whole lot for younger children (3-6), but don't miss Fantasmic (get there early for a seat).
As for the water parks, Disney Quest, Downtown Disney... I don't know if water parks are a must for you. I've always preferred Typhoon Lagoon, but only for a couple of hours. I have only been to DisneyQuest once, don't care to go again. Maybe if you have kids (or a spouse) that LOVES computer/video games it would be worth it. Downtown Disney is basically just shopping, and you can find everything they sell in the parks for the most part. There is a 24 screen movie theatre there in case it rains one day.