If the arduino mega is a little slow, any thoughts on using Adafruits new Grand Central as replacement? It's a lot faster, 32 bit, has the same layout and form factor. Only downside seems to be 3v logic. I've been thinking of using it when i get to the control hardware part. Thoughts?
Also i've been thinking of using uSteppers on some of the axis anyone has any experience with them?
I’ve been looking into using a faster processor also. I was looking at the Arduino Due, However it also operates at 3.3 V. I have only been able to find a couple stepper drivers that operate at 3.3 V. Stepper online is working on making a new driver that will be 3.3 V and more cost effective , They are supposed to be sending me one soon. I’ll post any progress on the blog if I get a system up and running with a 32 bit processor and a 3.3 V stepper driver.
It seems that at least the popular A4988 and 8825 support both 5V and 3,3 logic so at least smaller steppers can be driven without issue. Also both pivot and smart stepper support 3,3 and work with bigger motors. They cost a bit though.
I would think that the Arduino Due would be a good solution to the processor speed issue. The 3.3 V can possible be addressed with a 3.3V/5V logic gate optocoupler. I know that this would add cost and complexity to the system but it would also give you high noise immunity. Any thoughts?
3.3V ouput works well with 5V TTL logic but won't with CMOS.
The question is which driver use which logic.
My CNC use DQ542ma's driven directly by outputs of a cortex M3 (LPC1768) which is 3.3V. Wires needs to be short and the wiring is different: you provide common GND and the controller provide VCC to EN, DIR and STEP.
ADAFRUIT.COM 
USTEPPER.COM