In reference to bug #1918, the gns3.service.systemd file references ExecPath /usr/bin/gns3server which needs to be changed to /usr/local/bin/gns3server for the daemon/service to run without failure.
Please see the change I made to the service above.
Rewrote the systemd unit file to fix an issue where the system was not able to create a PID file inside /var/run.
I fixed this by having systemd create a new directory called /var/run/gns3. Then I had systemd change ownership of the directory to gns3:gns3 so the gns3server executable could read and write the PID file. I have tested these changes against Ubuntu 16.04.1 LTS.