JoeN:
Why can't some semiconductor company that specializes in microcontrollers step up and make one IC that does the work of both an 8-bit microcontroller and the microprocessor that these boards contain? Because it seems like a hack to have two parts and it certainly makes software development harder to write two pieces of code every time for one project specification. It seems to me that the Atmel part (the lowly 8-bit microcontroller) is there for the GPIOs, the interrupts pins, the ADC, the PWM pins, the timers, the I2C, SPI, USB, and serial ports, and the microprocessor is there for the large external memory and raw horsepower. Why can't that microprocessor get the lowly bits and pieces of the 8-bit part tacked on, and maybe a few DAC pins for good measure as well?
The BeagleBone Black (and other variants) have all of the described I/O functions, the Raspberry Pi has all but the ADC, and there are many others that aren't as hobbyist friendly.
One problem is that these devices commonly run a non-realtime preemptive multi-tasking operating system which isn't conducive to low level GPIO bit banging. The BeagleBone, in addition to its ARM processor has two on chip high performance (200 MHz/32 bit) realtime microcontrollers that can directly access all I/O, but programming them is non-trivial.
The logic behind the Yun and Tre is that they retain the accessible Arduino development system for low level processing while tacking on the high level functionality of a Linux based system.