What do i mean by this... well its the 2013 TDF and coming into the time trial i have been having some shocking stages... Wiggins 11'22" and Mollema 5'23" down even with the stupidly good team i have. But i would like to bring to your attention the results for the Time Trial, which is quite possible the only part of PCM i dont suck at...
1 Alberto Contador Team Saxo Bank 36'35 (81 TT + 98 Fitness)
2 Bradley Wiggins Apple + 1 (85 TT + 99 Fitness)
Im sorry but Brad is going to beat Alberto everyday.
Even with his age, Cancellara and Porte should have beaten Nibali.
This is where the game engine really shows its colours...
13 Andy Schleck Coca Cola + 1'23 (74 TT + 95 Fitness)
14 Luis León Sánchez Rabobank + 1'29
18 Alexandre Vinokourov Puma s.t.
20 Thomas De Gendt Vacansoleil + 1'36 (77 TT + 99 Fitness)
23 Tony Martin Omega Pharma + 1'42 (85 TT + 91 Fitness)
All Four of those behind Schelck could have beaten him in a TT only using one leg.
Tony Martin was beaten by everyone in the top 8 in GC apart from one person, despite most of them having lower TT stats than him, his fitness maybe low but he does not get beaten by Schleck.
The game engine seems to give big GC contenders huge advatages in places where they may not be as good.
I first noticed this in the Giro this year when i lost it because Rujano beat Kruziger in a TT for the win, which would never happen.
I think you forgot about the recuperation part. Sanchez, Vino, De Gendt and Martin can all climb, so I think they didn't take it easy in the mountain stages. Since Schleck has a much better recuperation stat, his final TT will be better.
As Vien pointed out, it's not purely the TT stat which has influence in the results of a TT after several hard stages. There's recovery, climbing (how much green bar the rider has spent - the better climbers spend much less/get much less tired), stamina, the fact that the contenders are usually protected in all stages while the others are either not being protected/doing the work in the peloton.. several factors.