My theory...
Armstrong decides to return in 2009, and do it clean. Realizes quickly he is going look silly, especially after Gila and the broken collarbone, so he goes back to the Ferrari well.
Ferrari has some new tricks up his sleeve. Bank the blood, microdose the EPO, but try this/these new drugs/cocktails. They help you lose weight and keep the power. Upside is that they are either undetectable, or not even on the WADA list, so you can claim to be clean.
The new drugs are very expensive, so only the elite have access, and only those who are working with Ferrari (Nibali), or can help Armstrong but not betray the secret (Horner, Levi).
Everyone else uses the "old" methods. Slowly word gets out about the newer compounds, but few can afford them. There is a three-way split in performance between the "clean" riders, the "old school" oxygen vector dopers, and the "new dopers".
Average speeds are down, because the domestiques on normal teams are now clean. In 2011/2012, Sky take it to a new level, and at least encourage the new methods to the Tenerife group.
By 2013, the elite are catching on that they too need to get thin with power. Contador either won't or can't follow. Wiggans doesn't like the risks he had to take in 2012. Cancellara slows or reverses his decline and looks thinner than ever. Riders with enough money and enough weight to lose, benefit the most.
Chris Horner: Domestique for Lance in 2010 in the Tour and still takes 9th. Crashes in the Tour in 2011 following an alien TOC and is out. In 2012, he places in the top 15 after fetching bottles for Frank and Klodi.
My guess is that Horner is using something that is not yet banned, just like Porte, Wiggans, Nibali, and Froome. I'm not convinced the Spanish Armada is using the same thing yet.
I think that the UCI knows what is being used, but is keeping quiet for now, because it isn't yet explicitly banned.
Horner will likely not win another GT, because the gauntlet has been officially thrown down. To win, you must (again) go full genius. The real war begins when Contador throws his hat back in the ring.