I guess the target demographic for Arduino was (is?) less technical people who wouldn't know JTAG from JAG. I've no problem with that, I think it's done a great service to the geek world.
on pins 11-13. Then MEGA was released and this was no longer true.
Why did they break this? With a quick look at the schematic there's no obvious reason the SPI could not have been run to D11-13. Although originally there's a PWM output on 11 and I guess they wanted all PWMs in a contiguous block. It also make sense to separate the SPI functionality I suppose. There often does come a time when you have to break a few things to get a better result.
Portability and standardization. (Sigh.)
There are obvious advantages to this, that's why there are 500-odd shields around. The trouble comes when you start with a 28-pin processor then grow to a 100 pin version with more features. You pretty much have to dumb down the new board and there will always be incompatibilities that cannot be reconciled.
Which brings me to the new Due. Will that be dumded down as well? Will we lose 4-bit SD and I2S because it wasn't on the Duemilanove or because they don't fit on the current header pinout? Will external memory be supported or is "50k more than anyone should need". And what about when the Due 2 comes out with a processor that has native HDMI?
The Arduino headers are essentially a bus and I guess this sort of issue has been a problem ever since 98% of the IO peripherals were stuck inside the processors. In the days of IO/memory-mapped UARTs etc all you had to do was provide address, data and control signal then add features later. All processors had these signals and the only real difference was the Motorola/Intel/Zilog style control lines and these could usually be standardised with a few gates IIRC.
I think it's more difficult these days, and I'm hanging out to see how they handle these issues with the Due.
Rob