I don't have a problem with Cavendish or Contador. Cav wins the sprint stages, Contador wins the mountain stages and the GTs, that's their domain. For me, the 3-4 breaks each tour are the domain of the rest of the peloton who can't sprint or climb, and that's what I'd like to see remain.
Did Thor win because he was stronger? Of course. But you know what -- Even if he didn't win, he's still the stronger rider. He and Gilbert will always be stronger then whoever wins from the break. Frankly, most breakaways wont win because the rider was the strongest in the peloton, but because he was strongest in a group that the strong riders chose not to have chased down or (be in the break).
If Strong riders tried to win every stage, they would, because they and their teams are just that much stronger. It doesn't mean they have to do on every single teams and literally leave 6-7 teams with nothing to race for.
I'm not advocating that every elite rider stops winning on their domain, but I do think a few stages every tour should be left for one of the lesser riders to win. Otherwise you leave them with nothing, and I don't like that. If you'd rather that those teams never had a chance, then fine. That's your preference. But not mine. And make no mistake - in a straight fight between the FDJ and Cofidis riders and the strong riders, the former have no chance.