I know Greece like the back of my hand, having spent a great deal of time there. I was curious about the comment regarding the ferry system. Most people I know take the hydrofoils/fast ferries. Not the shipping ferries carrying all the cars and bulk goods. Maybe you took a wrong ferry?
As for Santorini, the upper town is packed because cruise lines drop off their hordes 2x a day, but we rented a home for 2 weeks on the cliff below the main town of Oia, and it was quiet as could be. We avoid the cruise ship times which arrive the same time every single day. Otherwise, there're not many people.
Some of the most spectacular Greek islands are totally unknown to American and most worldwide tourists. For instance, Milos. It's an incredible place, and it's mostly full of Greeks and Italians. I still have no idea why people go to islands that don't have nearly the natural beauty of these places.