There are a few that are really fun. My kids were getting interested in gaming, so I had to have a look into suitable games. So here is a kid-friendly list of great stuff that runs natively:

GCompris: A lot of nice learning mini games for the very young (also good to teach e.g. usage of mouse and keyboard)

Minetest: Very similar to Minecraft, but with its own twist. Highly customizable with mods and completely free and open. I am running my own minetest server with a customized non-survival world that is used by my family.

Widelands: A really great community adaption (and extension) of the Settlers II. My son totally loves it.

Unciv: Civilization game based on the Civ5 ruleset. I actually had to deinstall it again on my mobile phone (also available for Android) because it has the same addictive properties as the original…

And for non-free games: Lutris + GOG makes me happy. Currently playing some older Tomb Raider game. Although not really native, I think. Probably using Wine or so…

Mindustry, sort of like factorio but open source and free on itch. Although you can also buy it on steam

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.

Kerbal Space Program!

0ad, Wesnoth, Endless Sky, Mindustry

I go back to Battle for Wesnoth a few times a year. There are many new scenarios over the recent years.

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!