First and foremost: don't stress out about all you may "miss". The way I look at it, there's never going to be a trip you see it all and that's what makes future trips exciting.

that said, here are suggestions for each park (and be sure to call WDW Dining for reservations): AK--It's tough to be a bug (maybe too intense for the 6yo). Dinoland, the safari, take the Wildlife express to Rafiki's Planet Watch (your 6y/o will love this) and Festival of the Lion King. Eat at Tusker House or the Rainforest. tip: avoid loitering on the paths when you first enter AK to look at the animals, birds, etc. You can do that on the way out. It gets very congested and you really want to get into the park and get on the major attractions. MK: walk through Main street (again, you can wander here as you leave) and go to Mickey's toontown for the character interaction. then work your way back through tomorrowland (Buzz, Stitch) and have a meal waiting for you at Crystal Palace (character interactions). then go through adventureland, frontierland and fantasyland.
EPCOT: the maelstrom ride on Norway is fun and Mexico has a boat ride that should be totally refurbished by the time you get there. Some of the other countries have movies which are excellent, but you stand during them and our kids weren't much interested at that age. Eat at Germany Biergarten for a unique experience and great buffet food that your kids will definitely enjoy.Walk back through the countries and spend the majority of time in the Land (Soarin and Circle of Life), Living Seas (Crush), and Imagination (Honey I Shrunk the Audience) sections.
MGM: must eat at the Sci Fi. It's Disney magic at it's finest. again, work your way from the back of the park and get to the stunt show early if you want to see it. That show is totally dependent on the weather, so if it looks rainy that day, don't bother. The muppet movie is wonderful (for all ages), Star Tours, Indiana Jones, ToT (maybe not the 6y/o?) but he could play on the Honey I Shrunk the Kids area. The evening Fantasmic is a must and don't bother with the meal deal--you shouldn't have a problem getting a seat. General advice, use fastpasses whenever you can. always make dining reservations--that way you have no hungry kids and no place to eat

save shopping and browsing until you are leaving each park. we do the majority of our shopping at Downtown Disney in one shot--the
Disney store there has most everything you see in the parks in the store; stay in the parks until closing and do repeats in the last hour when alot of folks have gone, and DON'T worry about what you didn't see--you will NEVER see it all. Enjoy each other and make some memories!
