Sounds like us. Our family is DD 6, DS 3, and DD 1. I know exactly what you mean wanting to have separate rooms for sleeping. We love to have this on our trips and always do. But like above posts say you will need to plan on spending quite a bit more for this luxury. Our new favorite place to stay is Bay Lake Towers right next to MK. The convenience of walking to Magic Kingdom or hopping on the monorail cannot be beat for young families. Especially your ages listed, you will be spending the most time in MK.
Cheaper villa options can be found at Saratoga Springs and Old Key West. An even cheaper option would be the Cabins at Fort Wilderness.
So the number one thing to plan is your resort budget and go from there!
We will be trying out the studio at the Polynesian for our family for 3 nights in August before moving over to BLT for another 8. I am curious to see how the resting/pool schedule works out with the one room arrangement.