One of the main problems with the route - which was actually first understood as an 'enhancer' of the Vuelta - were the 3 mountain top finishes in a row and the lack of a rest day.
Riders seem to become much more conservative/defensive every time, because they don't want to lose time. I also believe that many are riding at their max, and in order to sustain that for 3 weeks, you need to dose your efforts. Hence, when you have three uninterrupted, and seemingly exciting, mt finishes, GT contenders know they can't go full out every day, unless you middle name is "di".
If there is only a slight chance of a minor head wind, they'll hope for the next day (see Vuelta and TdF)
You saw Gesink who attacked in the last 1-2km, because he didn't want to blow up or use up a match for the next day. Contador on Verbier, Menchov for the bonus seconds on the first mountain stage in the Giro. Mosquerra, tried to get away, and he had to attack from far because his TT is below par. He never got more than 40s, including bonus s...
Perhaps a Giro stage a la block house, short, and a longish climb would be a good idea to alternate.
Or transition stages (easier ones) between big mt finishes.