And why is there that weird spacing between the two 8 pin connections?!
It was an design error that slipped in at the last moment in the rush to produce the very first batch of arduino boards. They either couldn't afford to redo the boards or didn't have the time to correct it, or both. Anyway once the design was released to the wild and lots of 3rd party shields started to be designed and sold to the public, it just became impossible to correct it without cause incompatibility for existing hardware already out there.
There have been several cleaver workarounds, you mentioned the 'bent pins' solution. Also some arduino clone board makers put in an additional set of shield holes with proper spacing, so that you just have to populate the board with extra header connectors and you can then use either the normal arduino spacing or standard .1" spaced protoboards. Example:http://www.seeedstudio.com/depot/seeeduino-v221-atmega-328p-p-669.html?cPath=132_133