There should be 3 Time Trial type stages.
The first or second stage should be a short (<10) prologue ITT or TTT to set gaps and orders.
There should be a pan flat one before the first mountains to set a gap for the climbers to chase and a second hillier one during or after the second set of mountains.
One should be long (40+k) the other should be medium length (15-30k).
So for example, you could have a 45k flat one on the friday of the first week, then in the second week have a MTT up Alpe D'Huez. In another race, you have a 25k flat TT before the first mountains and then on the last saturday you have a 40k TT hillier than the Grenoble one this year.
And you really need the flat TT before the climbs because bad-TTers really underestimate the amount of time they actually need.