There are some emphasis differences already present (flat stages earn more points than bumpy stages, which is again more than mountain stages)Indeed, dont we all? Its just a changing of emphasis that I'm suggesting.
And there is the "fatigue" factor that plays a part as well, going for a intermediate sprint will drain a bit of energy possibly preventing you from winning the stage (which is still pretty prestigious in itself as well)
But indeed - as mentioned before - the organization gives quite a bit of points in intermediate sprints to try to make it more interesting along the way
Only calculating finish-points Kittel would have a leading 135 points (3 x 45p for 1st place) vs. Sagan 115 points (2 x 35p for 2nd place, 26p for 4th and 19p for 4th).
However, it depends a bit on how to interpret the green jersey.
Some see it as the most complete sprinter others as the best sprinter (which in the past has often been the same, but many times hasn't).
A similar discussion could be held for the polka-dot jersey which often ends in the hands of somebody who has focused on winning the jersey (e.g. Virenque and many "unknown" riders who won it once) instead of ending in the hands of the best climber.