If shoes/boots are being worn with raw denim, they're presumably on the casual side of the spectrum, in which case I embrace the indigo stains. I agree with ryden, that spots, spills and "unnatural" marks bother me slightly. On my less casual boots, like the snuff suede WT Plaza boots, I am more careful with indigo as I don't want indigo stains on those. But reverse chamois will look better with some wear on it, imo.
10/28/14 at 11:00am