I have the same problem. I agree with andy hughes - i always travel with spare shoes, and normally only change into suit at last minute so its not creased etc.
I normally wear kitten heels. not only do they look smart but i also find i walk and stand better in small heels, which in turn makes me look better at the interview/appointment.
Luckily there are lots of stores with flat but smart and trendy shoes - office is great if you have one near you, failing that try dorothy perkins for comfy and cheaper ones, also next.
I wore clarks flat shoes when i worked long shifts at a hotel at uni, and although comfy i think they dont look as smart as small heels.
But most importantly you need to be comfortable so wear smart flats if you think you would be happier! Good luck!