I don't think they use time bonus enough, or they don't use them in the way that they could to make it more competitive. I think they should experiment with time bonus in such a way that someone who has better sprinting ability than a normal GC contender could possibly factor into the yellow jersey. I think of it this way. There are three classes of abilities in a cyclist:
1) Climbing
2) Time Trialing
3) Sprinting
Abilities 1 and 2 are both important for GC contenders. Ability 3 is usually not a factor. I would like to see GC determined by a balance of all 3 abilities.
Is this realistically possible? I don't know.