I think this Tour was cleaner overall. However I'm not sure about cycling in general. Earlier in the season we had disturbing climbs to Huy, Arrate, Kapelmuur and Sierra Road. The Tour, however, has the means to fight against doping more efficiently, and the AFLD was involved. Could it be that dopers have to be more careful during the Tour, ironically making it one of the cleanest big races? That's a possibility.
The numbers (times and watts) suggest the top guys are indeed going slower. As of late there's been a lot of emphasis put on what watts/kg ratios are possible while clean, and going above them is mighty suspicious. But then there's another side to that: the usual contenders may have to remain within these human limits, but nothing stops a lesser rider from rising from middle of the pack to great but human levels. This would be a sinister explanation for the close racing that has been praised as a sign of cleanliness.
That scenario would still allow the natural talents to shine, though. The general trend of improving French performances is probably a good sign in that regard, but "French cycling is cleaner" is not an absolute truth that will always apply, and I'm afraid the French and others may have become too complacent and lowered their guards. The improvement would be expected in a cleaner peloton if the French were indeed, as a rule, clean(er) these past few years (and all the data seems to suggest that), but that doesn't mean some particularly outstanding performances aren't suspicious. When whole teams perform above expectations, it makes you wary. Some French team might have decided they've had enough of being largely irrelevant and, on top of that, being mocked for not winning big races, while no one else followed their lead in anti-doping matters. It's always a possibility.
These two scenarios combined mean that we wouldn't be able to look at hard data, watt figures or climbing times to pinpoint outlandish performances, because they all would be within human limits. A top-class clean rider could produce 5.8 W/kg in the final climb of a mountain stage, but some guy doing it might still be doping to raise his power from a natural 5.4 W/kg or whatever.
So, to summarize, I think this Tour got clean enough that a very talented clean rider could compete, but there's still dark shadows overhead.