Wear your biggest, clunkiest shoes on the plane (usually sneakers take up the most room in a suitcase, so wear those).
With the rest, stuff as much as you can inside the shoes (things like socks and underwear stuff into shoes really well - you can really cram a lot of stuff in there!).
I'd rather bring fewer clothes (knowing I can always wash clothes or do a load of laundry) than worry about having the right shoes with me. I bring three or four pairs, different kinds (flip flops, sneakers, I even tried Crocs one trip). Believe me, shoes that feel comfortable at home may not feel so great when you're walking 8+ miles per day at WDW. A couple of years back, I planned to wear my regular workout shoes as my main shoes at WDW. Well, these shoes (that I thought were very well broken in!) gave me a big blister on the bottom of my little toe the first day of my trip. Thank goodness I brought some really comfy flip flops - I ended up wearing them the rest of the six days of my trip.