The spacing on the boards was a mistake. It was like that (I believe) before the shields even existed, and we've regretted it since, but each time didn't want to break compatibility. We don't even make / sell that many shields, and, anyway, a standard spacing would have made it easier to develop new shields, so it probably would have been better off from a business point of view. In any case, it wasn't intentional.
The Arduino team got so many decisions right that I am sure we won't begrudge you this one mistake. And its never too late to improve things, If your not selling many of the old shields perhaps it wont be difficult to switch to new ones evenly spaced 