I always thought it was a ploy to make people have to buy their proto shields which are significantly more expensive than a basic board you can buy at radio shack. perhaps I'm too much of a conspiracy theorist though.
No need for conspiracy - it was really an "11th-hour" screw-up; they were rushing to get the original (ATMega8) boards done at the very last minute to get the lowest pricing (and to get them done on time, I suppose), board designs were being altered left and right, and one of the main guys shifted one of the headers a bit and didn't realize it. It was originally supposed to be "standard"; must've been a real surprise when they got the boards back from the PCB place. I don't think there is any conspiracy here, just another example of what can happen when you don't take the time to do things right, even if it means missing a particular deadline (at least in this case, no lives were at stake).
It sucks trying to bend the header pins, I tought about filling the holes with JB weld and drilling new holes, you'd have to grind off the pads and run wires to the next row. All that said, it would be a pain, and the money you'd save probably wouldn't be worth your time and effort.
There are places out there that sell pre-bent header pins for this problem...
further proof it's a giant conspiracy among those who have the means to manufacture the PCBs - they price it just enough that building your own isn't cost effective.
Really, the prototype PCB shields (if you get the bare PCBs) aren't that expensive. Only when you start buying a complete "kit" (with all the headers, reset switches, etc) does the price start going up.
My biggest gripe, though, with having to use a custom-made PCB for a shield is the fact that I have to order online for the parts; I can't just run down, and buy it someplace locally (like I can for a regular prototyping PCB).
For myself, though, it isn't really that big of a deal - if you are making a prototype, you might as well just integrate the ATMega onto the board as a "standalone" Ardunio, and build the rest of the circuit nearby; use a regular Arduino for design and testing, then incorporate a separate programmed ATMega microcontroller into the final prototype...