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
I agree, I wouldn't be too hard on them for this one mistake. I probably wouldn't buy a freeduino with it fixed simply because if it's not an official standard anyway, I'm better off with an iDuino and a breadboard.
But I'd like to see the official boards switch to a standard spacing. In computing, backwards compatilibity is good, but every once in a while you need to throw away legacy support. Otherwise we'd still have 8" floppies and ISA slots.
The way they'd fix it in mainstream computing is with an adaptor. Have the new Arduinos on 0.1" spacing, and an optional adaptor to plug in older shields.