It looks great. I have a few small suggestions from the interface / software point of view, but I've asked the rest of the team (that knows more about hardware than I do) to take a look too. Again, I think this could be a great Arduino shield, and we'd like to work with you to get it made.
Did you consider putting two of the limit switches onto the pins with external interrupts (2 and 3)? That could allow a more fail-safe stop. Maybe the limits for the Z-axis, since doing only X or Y seems somewhat asymmetric?
What about making it possible to set all three steppers to half or full steps from a single digital pin of the Arduino, with the ability to override them individually with the jumpers?
Other than that, it looks good to me (with my limited knowledge of electronics).
Any thoughts on the layout?