You don't say when you are going but if it is a busy time of year I personally would spend my time at MK & MGM for your 1st trip. You also don't mention if you are staying on site. You also don't mention the genders of the kids!! Sorry, but I need details!!

Here is my recommendation, especially if you are staying on site or close enough to take a break:
1st day - am: MK Fantasyland & Toontown. Your kids can do everything in Fantasyland. They may be a bit scared at Philharmagic (my 4yo did not like the 3D at all so she watched w/o the glasses! My 4yo was also a bit scared at Snow White but managed to go on it 2 times!! Definately see the shows (Sword in the Stone, Cindercellebration & Belle's Story Time) & see the characters in Toontown. Donalds Boat & Ariels Grotto have some fun water stuff (plan accordingly). I would then take a break & go back to the hotel for naps (for the 2yo) & swimming (for the 4yo).
1st day - pm: MK Tomorrowland. You will be fine on Buzz, Astro Orbitor, Indy Cars & TTA (when you need a relaxing break). You can either eat in Tomorrowland or I too recommend CP for a nice Pooh character meal - the kids are the perfect ages & the food is good. Stay for Spectro (if it is showing ) & Wishes if possible!
2nd day - am: Sleep in a bit since you will have been out late the night b4 (well, late to your kids!!). Or if you really want to do a lot you can go to AK in the am. I would see Safari, FotLK, Pocohonotas, Dinoland (Tarzan show is too loud imho). Then back to the hotel for a rest/swim.
2nd day - pm: Get to MGM in time for the S&MC parade! Then watch VotLM & Playhouse Disney. Then depending on your children's preferences (boys or girls), you can see either Indy or the new stunt car show, Star Tours or B&tB. If they did not mind the 3d in MK, you can go to the Muppet Show too. Little ones really seem to enjoy watching the shows! There is a fun playground HISTK if they want to blow off steam. 50's prime time is fun as is Sci Fi dine-in! Stay for Fantasmic at night.
3rd day - am: MK Liberty Square & Frontierland. My kids were ok at HM (my 1yo was clueless & 4yo cuddled next to dad the whole time) & you may want to relax on the Riverboat. My 4yo loved BTMRR. Your kids may want to blow off steam at Tom Sawyers Island playground. If Country Bear Jamboree is still going on that might be fun too. Pecos Bill is good for lunch - great fixin's bar! Back to hotel for nap/swim.
3rd day - pm: MK Adventureland. Take the RR to Frontierland in time for the afternoon parade. Watch the parade & then hit Aladdin, PotC & Jungle Cruise (My 4yo's favorite!). Don't forget to get a Dole Whip! If you want you can hit the Tiki Birds. You may want to go to LTT for dinner for a nice character meal with Mickey & friends. If you didn't see Spectro or Wishes, be sure to see it tonight!
This is a pretty leisurely way to take your time in MK (2 full days). I hope this helps you plan your trip! Have a great time & be sure to post your trip report! Here are a few tips for kids of that age: Bring glow sticks from home. My 4yo dd wore hers even during the day which helped her on the "dark" rides and she loved them glowing at night (couldn't lose her either!!), bring some plastic soda lids - slip the stick of a Mickey bar into the straw holder to catch drips, if you do get drips, bring Shout wipes! My kids (well, the 4yo) loved getting autographs & pin trading. Bring bubbles in case you are stuck in line or while waiting for shows to start, my kids (as well as all the kids around us) loved popping the bubbles. Remeber to go at the kids' pace! Have fun!