Tom,
the problem with believing that shots should be given due to difficulty is that players do not always have the same difficulty on the same hole each time they play it so you can only generalize. In the end, due to this unpredictability any distribution of shots on a difficulty basis will be wrong in the actual context of the game most of the time. So you end up with an even distribution being the fairest over all with the caveats that have been added.
Jon
The subjectivity of "difficulty" is a key point, and I'd add that if the hole is extremely difficult for the scratch golfer as well, it may not be the place that a bogey golfer should be getting a stroke.
All of this points to the reasoning that the USGA provides (and I would assume the R&A does, too) in the link I've attached a couple of times already. It's critical that the handicap numbers be assigned based off of a large database of scores, so that subjectivity largely goes out the window and strokes are allocated where they should be.
And one more time: Strokes are NOT awarded based purely on the difficulty of the hole as determined by the overall stroke average. They are allocated based on the difference between what scratch golfers average vs. bogey golfers. While there is a high degree of correlation between that and the stroke average, they are NOT the same, and I've never seen a course where this wasn't reflected in the handicap numbers.