Brief walkthrough APU2 and APU3 schematics show below difference:
- power/reset/watchdog header changed
- LPC header changed to debug
- RXD3/TXD3 wired to PCIe x1 expansion
- SIM switch added
- use of mPCI slots explicitly specified
- fan control removed
- SIMSWAP pin added
- APU straps changed
- I'm not sure about mSATA changes, but it looks something is different
- internal us2.0 header added
- some PCIe connections removed (page 5)