Netserk already noted that time limits were extended a number of times this year. As a comparison, stage 20 this year and stage 10 from the 89 Tour were very almost identical in distance, route, vertical meters and speed, this year was 1kph faster. In 89, the time-cut was 12%, this year it was 20% because they extended the time-cut. It shouldn't matter if it came later in the race, stages have a set co-efficent, regardless of when they happen.
3-4 hours used to be the norm for the gap from yellow to LR. The last few years has seem it regularly reach 6 hours+. Why? If the guys at the front of the race are going faster than previous generations, then naturally the guys at the back should be doing similar. Therefore the time cuts should reflect this.