I'm not sure if you mentioned what time of year you're planning...if its anytime from May through Sept., I would recommend getting to your park-of-the-day early, and taking an afternoon break if you can. Just returned...and by 3:00, kids were hot and tired and really benefited from a swim and rest. And we saved money by eating off-site. We had a rental car. Magic Kingdom is a definite choice with lots of time spent in Fantasyland and Toon-Town. Don't overlook Buzz lightyear and the tomorrowland transit authority which will probably bore you, but kids seem to love it! It's a nice shady break also. My kids were less impressed with the Spectromagic Parade, so that's also a great time to ride rides because lots of people stop to watch the parade. Try to get a seat for Wishes at the Main Street Train station (up the stairs). When the show is over, you can easily be on the first monorail or ferry back to the TTC. My kids also loved MGM, with Playhouse Disney, Lion King show, Little Mermaid, and Honey I Shrunk the Kids playground. Al's Toy Barn is the place to get Toy Story autographs. It's good for a solid 1/2 day only in my opinion though. We really benefitted from the park-hopping option. We could do one park very early, take a break, and come back to another park for a nighttime show. It's also easy to take a break at Epcot from the MK, just hop on the monorail. Living Seas and Turtle Talk with Crush is amazing for the pre-school set. Also Journey into the Imagination w/Figment. World Showcase is great for strolling as well. If you're up to a character breakfast, Donald's Breakfast in AK is great. Try to get the 8:00 seating, so you can finish breakfast around 9:15 and already be in Dinloand which has some fun rides. The Lion King show, Flights of Wonder and Pocohantas are also great. Rafikis Planet Watch involves riding a little train to a petting-zoo type area, fun for them. Also the Kilamanjaro Safari is great for both your kids to ride.
Check out the height restrictions for all the rides in all parks. Then measure your oldest. We did a child swap at all rides that DS could ride. You get what is essentially a fastpass for the other parent to come back and ride the ride with the child who gets to ride twice. This is a great invention, and along with fastpass, made our trip so fun and time efficient.
Hope this info helps. Have a great trip!