While I agree that it sucks the arduono headers aren't spaced nicely for standard prototyping, I think this issue has been largely solved by the more recent versions like the Arduino Mini. I actually much prefer that form factor to the larger original one, as it fits in smaller cases, has less "fluff" (silkscreen, FTDI, etc) that costs more and isn't always used in development, and fits in a small space on a standard Porto board!

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.