With the release of the GNOME Shell 3.22 on September 21, 2016, the "Wayland Display-Server Protocol" became the standard regarding graphical user interfaces (GUI) on Linux.
Read more about Wayland at: https://en.wikipedia.org/wiki/Wayland_(display_server_protocol)
As a result, Minecraft is now running under the XWayland Compatiblity Layer. This results in an overhead and thus a decrease in the overall game performance in the sense of the FPS.
For example, the Intel HD 520 in Minecraft usually comes over 100 FPS. Under XWayland, only the half of this are reached.
Wayland: 1.12.0
XWayland: (xorg-server-xwayland) 1.18.4
A porting to Wayland is needed. See MC-92393
Minecraft currently runs with the compatibility layer XWayland, this is for legacy applications that don't use the Wayland Display Server Protocol, but instead using the old X11 Protocol.
The difference is, that MC-92305 and MC-92318 are two bugs describing problems when Minecraft is running on this compatibility layer.
Applications, especially games have an extreme overhead, if they are running on the XWayland compatibility layer.
Other games using LWJGL are starting without problems - and Minecraft is using an old version of LWJGL.
Maybe it is because 2.9.1 is too old, and don't have Wayland fixes.
So maybe update the LWJGL Library for Minecraft on Linux?
Have you read my bug-report?
"Other Java Games that are using LWJGL are running fine with the Wayland/XWayland Display Server Protocol (Nuncabola etc.)."
Other games that using the LWJGL Graphics Library are starting fine and having almost no bugs on Wayland.
This is not a technical support issue. Please re-open this Bug-Report.
Wayland is the new Display Server Protocol for Linux based Operating-Systems. It replaces the X11-Display Server Protocol.
Wayland is the new reference-implementation of display servers on Linux based Systems.
More and more Linux Distributions will ship Wayland per default in the next months. So all users using modern Linux-Distributions will have this problems in near future.
I've updated the affected versions. Still very important issue.