As the title says: What is the best native Linux games?
I know you are specifically asking for natives, but with the awesome work Valve has put into proton so many games play well with linux now!
Mindustry, sort of like factorio but open source and free on itch. Although you can also buy it on steam
Slay the spire and borderlands 2 are great but borderlands 2 doesn’t have all content available on the native port
0ad, Wesnoth, Endless Sky, Mindustry
Kerbal Space Program!
Don’t know about them being the best, but I’ve been playing Valheim and Shadow Tactics: Blades of the Shogun and having a good time with both.
The Talos Principle must be mentioned here. It was the first major game to provide Vulkan support, running just incredibly well.
And of course, Minecraft.