It adds more excitement to the first week - regarding sprinters chasing the yellow for a day (which they deserve, as they're the dominant riders of the first week).
Those saying it falsifies the result - the same goes for the group getting the same time. Obviously the argument here is for safety, however at the end of the day Cavendish is still going to finish well ahead of Schleck in a sprint stage - even disregarding all safety aspects.
It also means you see the sprinters have a crack in the prologue - which adds to that event. As it is, the prologue is basically only contested by time triallers and prologue specialists. Loads of sprinters are decent prologue riders who can figure in the top 10-20 in that stage.
At the top of mountain stages they shouldn't be too big - you don't want to give someone a big bonus just by out sprinting their rival - as generally you get much less 'grouping' by the commissaires on mountain stages anyway. But some small bonuses just to split up guys on level times etc would be nice.