Disadvantages of ATXMega

• Runs at 3.3V only, no 5V tolerance
• Requires a compatible bootloader, flashed via a PDI interface
• Requires special implementation of Arduino software
  
  • Most of the support is provided by the 'XMega For Arduino' project
  • Some libraries still need porting
  • Not much support outside of the project
• Not all of the processors are properly supported by existing compilers and tools
• Certain things (like interrupts) force changes to the Arduino API to support them