For starters the Leonardo introduced a few changes to the pin layout upon its release. The ones relevant to shield compatibility (which we handle) are:
The I2C pins were changed from A4-A5 in the older Arduino’s, to D2-D3. The SPI pins which were in pins,11,12,13, as well as the ICSP headers were removed from pins 11,12,and 13. SPI can only be accessed through the ICSP headers in the Leonardo.