Are the GC guys clean? No, but they are cleaner. Any rider in the top five from the 2007 Tour or Giro would have won this years Giro, no sweat. My point earlier, was when riders who have been heavily doped, drop off the juice and can only safely (not get caught) take miniscule amounts compared to their past, they will get slower. The augmented level of power they are capable drops. Doping benefits are not uniform. Some people get more benefits than others.
What happened last year? All of RadioShack were made to look normal, even clean. Why? Because last year cycling really started to look cleaner. Thus it makes a lot of sense to me and doesn't come as a shock that Contador is better than the other GC guys. If he can get away with an extra level of doping, others certainly have the means to do so as well, alas, he still wins? Typical catch 22 situation. Damned if you do, damned if you don't.
Of course power outputs tell a great deal, but we can tell they are significantly slower than previous years. Oddly enough though, there are still gaps between various riders, even though everyone's overall times are down. Why? It's always happened, skill and maximal physical output follows a bell curve, regardless of clean or doped. The maximal has dropped, but one or two guys will always be several standard deviations to the right of the mean. Those guys will always be questioned, sometimes incorrectly, other times justifiably.
Power outputs tell a great deal. Over 6.3 W/kg, do that for more than 10 to 15 minutes without huffing and puffing and you are clearly juicing. Long climbs, 30 to 40 minutes, you do over 6.1 W/kg, you are also juicing. Take the Shack last year, Chris Horner dropped some power figures for when LA crashed at the Tour. Apparently they were doing 5.9 W/kg and the time gap to the peloton remained the same. We later found out, that was because The Sorensens were setting the highest overall power output for the entire Tour, a pace that cracked everyone bar Contador and Schleck. I think from memory it was around 430W for 6 minutes.
As I said at the start of this reply, go back 3 or 4 years and take any top 5 GT GC rider from those years and transport them through time and put them in the same form against todays peloton, AC today. They'd beat him thoroughly. That doesn't mean he's clean, but he is cleaner. It's about perspective and remembering what has been done and questioning it's relevance to today. Does it show something useful? Take all the doped riders caught, Sella and Di Luca. They're normal now. LA looked normal last year. Then question why? They have many reasons to not dope. What happens when they don't dope or tone it down? They get closer to their natural base level, of which there was early career evidence they were not GC riders, hence their lack of current GC status. I need only look at Cadel Evans this season and last winning a lot more to realise something has changed. I consider him like AC to be one of the few exceptionally gifted natural talents, guys who always rise to the top, be it cleaner but still doping peloton, or uber doped peloton. In a cleaner peloton, augmented lesser talented riders can no longer sneak wins, hence the more naturally gifted win more often. I expect to see a lot more of this happening, especially when Valverde returns next year.