As far as I understand Fusion 360 is Windows and Mac exclusive. EAGLE currently supports Windows, Mac and Linux.
Now that Fusion 360 and EAGLE are probably combining into single product (at some future date) what is the future of Linux support in EAGLE?
As far as I understand Matt Berggren, they will not drop Linux support. Check this podcast:
I received the following answer Autodesk support regarding the availability of Fusion and Eagle on Linux:
"According to our product specialists, Fusion is available on Mac and Windows only. Since Electronics is a part of Fusion it will work on these two systems. The current stand-alone EAGLE also supports Linux. As long as EAGLE will be available it will be on Linux, too.
In addition, Fusion 360 does include an entitlement to Autodesk EAGLE. Autodesk EAGLE is a stand along application which will continue to support Windows, Linux and Mac. At this time, Autodesk EAGLE and Fusion 360 have a bidirectional workflow. Fusion 360 is able to run on Windows and Mac operating systems."
So in summary it appears that Autodesk intends to support Eagle on Linux as long as Eagle is available as a separate product.
I think the problem could end up being that development focus will shift to the new integrated ECAD in Fusion 360.
So Eagle will continue to be available and run on Linux, but it will (gradually) morph to a kind of "maintenance mode" with little new development.
I would like to see Autodesk work on getting Fusion 360 support on Linux through some method. Either their web interface (which at the moment is far too limited) or semi-official support for the desktop app through wine.
See this carefully considered suggestion for official wine support: