I wonder if the answer doesn't somehow involve encouraging people to venture out of the big European cities and into the surrounding areas? The article touched on that idea, but it could be the key.
Whenever I visit Europe, I tend to split time between major cities and smaller towns/rural areas that I typically drive to. I often find the towns as charming and memorable as the capitals, and there is far less of a tourist presence. Quite often they are completely devoid of tourists.
As for cruise ships, I don't know what to do about those. I feel badly for any smaller city that gets regularly visited by these overwhelming behemoths.