Maybe if we didn't seem to get one in almost every GT it wouldn't seem so played out, but frankly they belong on the track and should never have left it.
As to them affecting the GC... Michele Scarponi lost more time in the 32km TTT in the 2010 Giro than he lost in the other 3453km combined. By about four times. In a 32km ITT, there is no way, no way on earth Ivan Basso takes more than 2 minutes out of Scarponi.
TTTs are, however, here to stay. If the 2009 Tour didn't kill the TTT off for good, nothing can, sadly. Here's the top 4 teams in the TTT that year:
Astana
Saxo Bank
Garmin
Liquigas
Here are the teams for the top 10 on GC that year:
Astana
Saxo Bank
Astana
Garmin
Saxo Bank
Astana
Liquigas
Garmin
Liquigas
Française des Jeux
By the time they got to the Alps, riders who didn't have super-strong TTT teams were already eliminated from contention, allowing the strong TTT teams to tighten their vice-like grip on the race, which they had because they, surprise surprise, were the strongest teams. Riders on the strongest teams are already advantaged by, you know, having the strongest team.
The arguments for more or less boil down to two things.
1) they look cool. I don't disagree, but aesthetics is a poor return on the effect they have on the GC;
2) they force teams to select more balanced teams, meaning fewer mountain domestiques and more km raced alone by the leaders.
Point 2 actually has some merit, but I don't see why they can't just include tougher rouleur stages, with some cobbles and the like, instead. After all, anything else a TTT has to offer can be replicated, only without most of the flaws, with an ITT.