To throw in my two cents, having completed several books of Nikoli Sudoku puzzles as well as some of Pappocom's over here (most recently, Grand Master Ultimate - not sure how the UK offerings differ, but this is the name of the title in the States), I think both puzzle creation methods offer different things.
I do not think that many of Nikoli's puzzles, even in their hardest collections, reach the level of difficulty of computer-generated puzzles. This is not to say that all hand-written puzzles are easier as I've seen some that are very very hard (in fact, some of Tetsuya Nishio's super hard books such as the one I'm currently working on are probably a great counterexample to the statement that hand-written puzzles are easier). Its just that, in the printed books I own from Nikoli and from Pappocom, I've spent the most time solving the Fiendish ones in Wayne's books than I have on Nikoli's, even in their Gekikara (Super Hard) Sudoku series. Computer generated puzzles can more readily, I believe, be forced to have a particular kind of step required in their solving. As a solver who tends to never list all candidates in a cell (I solve for speed and minimize pencil marks to what I consider "useful" information), there are some techniques computer-generated puzzles require that are harder for me to see. They are not unreasonable techniques to require in a sudoku, just not ones Nikoli puzzles tend to have. It may go back to Wayne's point about what is a reasonable and an unreasonable puzzle to have someone solve on paper but, as Nikoli's puzzles tend to be more "reasonable", they may seem in most of their forms to be easier.
On the other hand, there is something tremendously organic and esthetically pleasing about Nikoli's puzzles. It is not, as mentioned earlier in this thread, just the shape of the givens in the grid. For some of their puzzles (not necessarily all), one of two things is true: (1) the number placement within the shape placement is fundamentally beautiful - admittedly gimmicky, but there is a repeated clustering of numbers in a repeated shape, a way that the center box is framed with diagonals that repeat the same number, etc. - that is not something computer-generated puzzles ever tend to have. Just by looking at a puzzle in class (1), you can tell it was likely hand-written and I'll make it a Turing test for sudoku for when a computer-generated one can have the instant esthetic beauty of a good hand-written one. (2) The look of the puzzle may not seem that special, but then the solving of the puzzle shows that it is. As an example off the top of my head, there may be a particular symmetry in the solving route that you use to answer the puzzle. There may be a trick such as a pointing pair to get information in box 8 that then solves a number in box 7. On the other side of the puzzle, the same exactly placement and rule gives information in box 2 that solves a different number in box 3. This kind of logic then propagates around the puzzle in an interesting spiral. While computer generated puzzles may be symmetric, few have been set up so that the solution also follows a symmetric path. On the other hand, it often feels like many hand-written puzzles have something along these lines. There is then the rare puzzle that combines both feature (1) and feature (2) and these will only, at the moment, ever come from hand-written puzzles. These tend to be too gimmicky to be "hard" puzzles. At the same time, I'd say they are very fun sudoku to do and what I would suggest someone who hasn't done many before try out as they may catch on to the "voice" of the author telling them what they should be looking for as they continue to make progress. I never think the computer-generated ones are hinting to me at how to solve them - I'll end up just going down my list of solving techniques (check each digit for any information, check rows, check columns, etc) until they are finally solved.
I would say the above argument holds - perhaps even better - for many many other logic puzzles that can be either computer-generated or hand-written. From slitherlink to masyu to fillominos to nurikabe, there are "gimmicks" that are rare, but special, in the hand-written ones that will not come from random computer generation.
Thomas Snyder