Also we have the element of chance often removed from the races now; with one notable exception in the wind and rain in 2010, the GC contenders all know where each other are at all times. The quality of domestiques has gone up thanks first to Banesto then USPS and Telekom, so that long range attacks are increasingly likely to be futile, so regularly everything comes down to the one climb or the one ITT; and with that one climb, the riders are better protected by their domestiques so they're fresher and more able to keep up, thereby gaps are smaller.
Another problem is the continual search, less by the Tour, but more by the Giro and Vuelta, to find bigger and harder climbs. This means that sometimes when you have two heavy mountain stages back to back, riders are reluctant to leave too much on the road on the first day in case they don't gain enough and lose it tenfold the next day. The Tour doesn't bother with searching for new hard climbs, it just sticks a keynote climb that will get all the pre-race hype there instead.
Also, over time the gap between the pure climbers, the rouleurs, and the GT contenders has been increasingly blurred; there are only a handful of examples remaining of the old-fashioned pure climber who lost minutes upon minutes in every ITT - Joaquím Rodríguez being the most obvious example. Even people like Andy Schleck, Carlos Sastre and Igor Antón, whose ITTs are regarded as suspect, limit their losses incredibly well in comparison to some of the mountain goats of the past. Of course, the problem can be flipped over, in that so many ITT specialist riders were able to become mountain goats thanks largely to the glory of three letters that were popular in the 1990s, that the amount of ITT mileage has had to come down in order to allow the mountains to still be decisive even as the gaps created by them decrease.