You said "other than traditional batting" -- so I won't suggest types of batting. Honestly, why not just make him a coverlet rather than a true "quilt"? A coverlet is 2 layers with quilting (I've always seen them with 2 layers of quilter's cotton -- or sometimes one layer of linen & one layer of cotton if it's for an adult bed. Sticking with cotton front & back will keep it cooler than backing with flannel). They are very popular in warm climates like Costa Rica & are every bit as beautiful as a "quilt". Unless you are planning to enter it into a competition, there's no rule that says you have to have 3 layers in order to quilt it.

Also, keep in mind that the more densely you quilt it, the heavier (and hotter) it will be. With a 3 1/2 year old, you need to quilt it closely enough together that it will hold up in the wash (generally, that seems to be no more than 2" spacing) ... but I probably would try to choose a design that is at least 1.5" apart so that it stays soft, drape-able & cool.