[steve918]

and the weird staggered header design was a mistake from the very first boards that has just continued to carry on through the years.

[jffry]

According to [1], the decision to keep the spacing for compatibility reasons was a conscious one. I can see how they might want to keep the whole ecosystem of Arduino-compatible accessories/kits/etc functioning.

[1] https://electronics.stackexchange.com/a/941