Armstrong in Context:

So what can one conclude from all of this information?

The fact that the performance of cyclists exhibits a broad peaking in the mid 1990’s is consistent with IPETs being used extensively in cycling during that period. The use of IPETs was not isolated to individuals, but appears to have been pervasive throughout professional cycling. The fact that speeds and climbing rates are reducing as a function of time points toward the success of stricter doping controls in the sport.
The reduced variability in performance indicates that natural ability, while obviously required, has been reduced in its impact upon determining success, and this appears to have been the case since the beginning of the 1990’s. (Comments about how EPO can reduce the impact of natural differences on performance among different riders, along with other discussions, can be found in Ref. [11].)
The data are consistent with Armstrong, upon his return, not doing anything obviously different from other elite cyclists in the TdF, though obviously, he just did it a little better. This is the “level playing field” scenario.
The data are consistent with the assertions made by LeMond regarding doping in cycling.
Finally, it is worth mentioning that the data analyzed in this work is but a small fraction of what could potentially be analyzed. One of the interesting features that was touched upon only in the analysis of the TdF prologue data, is the complete distribution of riders speeds in each event. If, in fact, IPETs that minimize the impact of natural ability in performance are being used, this trend should be clearly evident in the distribution of speeds in any given single event.
To close, the data that has been analyzed in this work points to the combined natural ability, race preparation and recovery of post-1999 Armstrong being consistent with, but slightly better than, other elite cyclists competing at that time. The strength of Armstrong’s performances in the collective events suggests that his preparation and recovery methods were shared with his team-mates.

My Thoughts (given these observations and conclusions)

If one is convinced that IPETs were used extensive during the period from the late 1980’s forward to today, it makes little sense to remove titles from those who confess to using IPETs, as there is a high probability that the runner up, who would be awarded the title, was also using IPETs in essentially the same way. I suggest that it was a mistake to strip Riis of his 1996 TdF title because each of the 9 riders below him in the general classification (GC) were also likely using IPETs. Further, it is likely desirable to create an environment in which offenders from the past can confess to using IPETs in past events as this may help in the development of future anti-doping protocols.
Stripping Armstrong of his titles, and awarding them to the runner ups, has the same problem discussed in the previous bullet-point. Given the data as presented here, and the fact that multiple members of his teams have admitted to using IPETs, it seems that there is high likelihood that the runner’s ups (through many placings in the GC) were also using IPETs.
If titles are stripped from Armstrong, then, in fairness, similar investigations should be launched against Indurain, as his performances have similarities to those of Armstrong. This could be generalized to all TdF winners since 1990.