Yes, wheels make a difference. Good handmade wheels will help, but if your frame is small and aluminum like my Cannondale they will improve the ride. I gave up on aluminum and bought and Aegis "Swift". It's carbon fiber, handmade in Maine and only made in small sizes. With my Mavic Open Pro wheels the ride is awesome. The neat thing about carbon is that the materials can be manipulated, the softness and stiffness can be built in where the rider needs it. Aegis built the Swift with small riders in mind. I feel none of the stress I used to feel on the Cannondale
BTW, Trek does not make cf frames in small sizes.