Plus there are many versions out there within the arduino ecosystem, including larger pin count ones, faster processors, and even ones that use non-Atmel chips like the Teensy.
There was a problem, and It's been solved.
While I agree that the ecosystem has provided solutions, I would have to respectfully disagree with your conclusions.
Had the problem been solved, we would not see new SoC and microcontroller platforms (heck, I think there's even an FPGA dev platform out there too) that continue to supply properly-spaced headers for this issue.
Doing so continues to perpetuate the problem, not solve it, in my opinion. A real solution would be to fix the issue (ideally, by the Arduino team), and there being a push to adopt the new layout/spacing. Perhaps an adaptor shield could be created, too, for legacy support.
Honestly, this should have happened immediately after it was found to be an issue (which likely would have been seen a long time ago with the early ATMega8 RS-232 boards made for the educational classes or whatever Massimo made the boards for originally); it should have been corrected there and then, with the next iteration.
But, history is history, and there's nothing we can do but lament, learn, and move onward...
That one, oh-so-minor difference is a thorn in many a uC experimenter's side, because it means that standard 0.1" spacing of pins to make custom shields is impossible without special thru-pin headers, bending pins, third-party thru-hold blank shields, or just leaving one or the other header off entirely (which isn't a real solution if you need one or more pins on both headers).
We could have seen a ton of custom 0.1" proto and strip-board shield designs, but instead we are thwarted by this one simple mistake caused by being in a hurry due to a deadline.
Now - we are stuck with it - likely forever, because each new iteration of microcontroller hardware almost guarantees that there will be support for "Arduino Shields" because so many are out there. Yes, I know there are experimenters "blank" shields - but they are rarely as inexpensive as a standard 0.1" PTH PCB - and almost all of them are the size of a single shield, none larger.
It would have been nice, for instance, to be able to put in extra-long pin headers on an Arduino, then plug that on top of another larger PCB with standard hole spacing (whether soldered in-place or via headers too). Instead, the only option is to "build" the Arduino onto such a custom board (ie, program an ATMega328P and plop it on the board with resonator/crystal/power/etc).
/sigh/ - oh what could have been...!