The -Lite edition significantly simplifies the board to reduce the cost. It removes a few features: gone is the level translators, external PLL chip, and the FPGA moves from a LX25 to a LX9. This means a few features such as the analog and digital pattern triggering is removed to fit into the smaller FPGA.
The -Lite edition integrates everything (Target & Measurement tool) onto one board, which makes it a better target for use in training courses. There are no jumpers to set, so along with the considerable size difference it's more reliable.
The -Lite edition improves the USB interface. The XMEGA programmer is now part of the same chip as the rest of the USB interface, which means you only need a single USB cable.
In addition the -Lite edition has improved glitch generation abilities - it has a high-power MOSFET which can be used to directly glitch targets such as the raspberry pi.