The Arduino is somewhere around 2.5 to 3 years old. It might last anther 5 to 10 in a usable form. Now would be the time to rationalize the form factor before even more shields get created.
This is the exactly the same issue as the (lame-brained) Apple one-button mouse, or maybe even worse, the disk-eject menu item that was in the OS for 10 years which all Mac users knew to avoid because of the disk swap nightmare.
Apple never bothered to fix the menu item and it was just a useless pimple on the Interface, or worse if a newbie used it and got caught.
Bad design decisions get embedded in things and then everyone must live with them (and laugh / swear at them) for years to come, because the company cannot bite bullet and admit they made a mistake. Apple was so embarrassed about the one-button mouse that they had to preserve the one-button design look even while (finally - 17 years later) going to a two button design concealed under the one-button look. Everyone's just trying to forget the hideously unergonomic (and beautiful) round mouse.
Conspiracy theorists have suggested that Arduino team deliberately created the off-grid design to make their hardware incompatible. Does an official explanation from the team exist of where this odd quirk came from?
One example of the awkwardness that this [disfunctional] standard causes is an NKC board with both sets of headers to accommodate the (sensible, standard grid layout) and the Arduino system. I'm sure the design will work well enough, but it's ugly and just shouldn't be necessary if the Arduino design was a rational layout.
But in the mean time, just think of the off-grid quirk as the Arduino Team's one button mouse and maybe start looking around (and developing) other standards (such as the two or button mouse wth scroll wheel that seems like it's become the [sensible] defacto standard).
One sensible thing to do would be for the people developing Freeduino hardware to get together and discuss / standardize some new form factors, if enough units of a new form factor are producted, that work in a sensible way, the Arduino team will eventually put out a two button mouse, but maybe it will take 17 years.
Maybe it could even start a discussion about collaborative design of open-source hardware.