Dear Wendy,
I have never made a 2 layer quilt. So, I'm a bit bias. If we're going for warmth, then rag quilt with batting sandwiched with flannel on both sides. Our 100% cotton quilts (with 100% cotton batting), don't seem to provide THAT much warmth, so I refer to them as summer quilts. In home that's kept at 70* year round, rag quilts are used year round as well. My vote is for 3 layers.