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.