I'd do a search on AirBnB, if you don't mind staying a few minutes' offsite and driving to the parks -- there are many AirBnB options with multiple bedrooms decorated in kid-friendly Disney styles, playrooms, etc., and some are located in complexes with elaborate pools, water play areas, playgrounds, lazy rivers, etc. Many of them are offered at half of the price of many onsite options.
If you'd prefer to be on Disney property, I would stay in a standard room, many of which have fold-down Murphy beds or a foldout sofa if the kids aren't able to share a bed. When our kids were little, we'd all go to bed at the same [early] bedtime at WDW because we were all so worn out! If DH and I couldn't sleep, we'd step out onto our patio or balcony (where available) to chat and take in the views, while still being able to monitor our kids through the sliding glass door. If you're sure you need a second bedroom to have one child go to sleep early and undisturbed, I'd look into the family suites at Art of Animation or All-Star Music, with an eye toward putting the 2-year-old to bed on an air mattress or other improvised bed in the master bedroom so the rest of you can enjoy the "living area." after they've gone to bed.
The fact is, Disney's offerings for onsite suites are really poorly-designed for families with young children. In addition to the enormous cost, any accommodation with a single separate bedroom (e.g., Art of Animation Family Suites, All-Star Music Family Suites, 1-bedroom villas) generally intends for that bedroom to be used by the parents, with the kids sleeping in common areas on foldouts, meaning there's the danger of older/taller kids unlocking and slipping out the front door or onto a balcony while Mom and Dad are sleeping, and once the kids are in "bed," nobody can use the kitchen/living/dining areas without disturbing them...
(*EDIT: I see someone above mentioned the Cabins at Fort Wilderness. That's an excellent recommendation, and because there are sleeping spaces for the whole family in the master bedroom, it avoids the design flaws of the Family Suites! I'd give them some serious thought.)