If you are ever in Portland Oregon and would like to try both units with a person that has lots of experience with both of them give me a call. We are located about 5 miles from Van's and have both an IFD540 and GTN650 in my personal RV-10.
End user firmware updates
Avidyne has always made every IFD540 firmware upgrade available to end customers at no charge.
User defined holds
Avidyne has always had it in the IFD540.
Ability to fly radius to fix type approaches
While the IFD540 has the accuracy to fly RF approaches, the bigger issue is that RF approaches require the pilot, aircraft and FMS to be certified to fly RF approaches. Recently Garmin added support for RNAV approaches with RF Legs, but it still has a bunch of caveats:
https://bruceair.wordpress.com/2016/03/18/garmin-gtn-avionics-and-rf-legs/
Ability to load another approach while flying a missed approach segment
Avidyne has always had this available on the IFD540, you can load many more than two approaches.
Dynamic curved flight plan segments based on speed
The IFD540 supports this
Animated NEXRAD for those that have weather receivers
The IFD540 does not currently support this.
Real time fuel range rings
Avidyne has always had fuel range rings on the IFD540.
LPV+V support
Avidyne added LP + V support to the IFD in July 2015.
Advanced airway navigation including preview capability
The IFD540 has always had procedure preview that actually lets you see the preview before you load the plan, not after the flight plan has been loaded.
Remote control/integration capabilities
Avidyne and Dynon/Advanced Flight Systems have and will continue to work together to create better system integrations. If you have noticed already, the AF-5000 EFIS has the same flight plan coloring as the IFD540. The IFD540 also has a number of remote control features with the remote Bluetooth Keyboard that are very useful.
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Rob Hickman
Advanced Flight Systems Inc.
N402RH RV-10