Would moving to a TI Stellaris or STM32 (ARM Cortex M4 based boards) or Renesas RX (not quite BeagleBone power but considerably more powerful than the AVR) make sense? I have not looked at the firmware yet but I wonder if coding the firmware in C/C++ and using an RTOS would help in terms of real-time control priorities, for example, managing the temperature controller and four axes of stepper control without other items (such as LCD display or control input) affecting real time operation?
I think embedded Linux may be overkill, but certainly an RTOS like Micrium MicroCOS III would be useful, though there are some modest fees. As for embedded Linux on a platform such as a Raspberry Pi or Beaglebone, it makes sense to use real time extensions such as Xenomai.
The one place where I see Arduino shining is the bootloader capability, but it's possible to build a USB or serial bootloader.
I think the most important questions are:
(1) does the Marlin firmware allow for tight control of the nozzle temperature even under worst-case load?
(2) does the firmware allow for the appropriate control of the motor axes even when a user is controlling the interface to prevent any kind of plastic overflow or starvation?
If the answer is yes, then the Marlin firmware meets the general requirements. I've seen a couple of bugs where I have to power down the unit to reset it after I tell the unit to stop printing-- it still says "printing."
Josh Karch