While the Mk1 design actually had very few issues and pretty much worked right from the get go, there's always a few things you want to change once you actually get to play with some hardware.

Firstly the known issues with the Mk1 design:

• Mis-read of datasheet on FTDI232 chip (yes it can run on 3.3V......but only if you provide your own clock!!!  - otherwise it needs 4.5-5V Vcc).   So a re-tracking of 5V rail to support this.
• I2C: SCL and SDA are swapped relative to the intended layout of the dedicated I2C header (so correcting this)
• Pull-up resistor for Xbee TX line: Without this mod you'd always need the Xbee plugged in to get UART1 to work.  Fixes this inconvenience.
• JTAG RST line.....not actually connected to RST (you can work round it, but not ideal).  This was intentional in the original design, but have now found some JTAG's are really fussy about this capability to assert the SRST (RST) on the board.
• Silkscreen was pushing the limits of the PCB Fab house.

Plus the following enhancements:

• Diode protected USB power - to allow development using only the USB port, instead of currently needing USB + battery if you want to work with the UART1 (via FTDI chip).   This is mostly a convenience issue, but it does make the board more green also as you'll use less batteries :-)
• Re-tracking of the Servo Power rail will allow these connectors to be used to drive servo's, or to use a similar 3 pin header but without delivering 5V to the target.
• JTAG pin-out redesign, to support the 10 Pin JTAG ARM standard.
• Slight tweak of the Analog (Port C) pin-out to support Sparkfun Razor 6DOF board to allow for IMU applications.

As you can see below, the Mk.2 design is well advanced and in the final review phase prior to being sent out for fabrication.