The organisers of the TdeF have quite a bit of experience in this sort of thing and they still tinker with the rules to try to improve things. The underlying reason for the time limits is that if you didn't have them, riders with no interest in the GC could take things easy on some stages, conserving energy for later. There has to be something to make everybody race every day.
GC riders don't need this incentive because their overriding aim is to avoid losing time.
I only remember one big injustice, although there must have been others. I'm not going to resort to the internet to remember the exact date, but it was in the Armstrong era when Eric Zabel regularly won the points competition (something like six times.) FWIW, he was a pioneer of the sprint train. Anyway, during one stage, Stuart O'Grady was in a long-distance breakaway and as he was no threat to Armstrong, there was no chase. A lot of riders - almost everybody - finished outside the limit, but an exception had to be made to the rule or the handful of riders in the breakaway would have been the only ones left in the race. However, O'Grady, who was a serious contender in the points competition, was tired from his breakaway efforts and he lost out in that competition.
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From viewers' questions over the years, I get the impression that some people think that riders who are not specialist climbers are somehow too weak to get over the mountains. I remember somebody suggesting triple chainsets with a granny gear. These are very strong riders, but their build means they cannot climb so quickly as the lighter riders. It's a stage race and the trick is to get a balanced route to give different types of rider something to aim at.
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Vincenzo Nibali's team has announced that he has abandoned.
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