There are several hotels in the WDW area that have 2 room suites. Doubletree Guest suites near Down Town Disney is probablly the closest. Near the Crossroads is a Residence inn, they actually have a one bedroom condo style, with a full kitchen. That may come in handy with a toddler.
Try some of these:Comfort suites Maingate East, Hawthorn suites, Buena vista suites, Caribe Royal Suites, Quality Suites Maingate East and Homewood suites.
Another option may be Tropical Palms. They have small cabins located in a campground. These cabins are self contained, with a full kitchen and a separte bedroom. There's a pool there and they seem quite "tropical". I am sure there are others that I have missed... do a search and most of these actually have floorplans that show a separate sleeping area.