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

@privsecfoss Starsector has a Linux build, and is an excellent game.

FTL

0ad, Wesnoth, Endless Sky, Mindustry

Kerbal Space Program!

The games I keep coming back and playing since years are Factorio and Cities Skylines. And Minecraft if you call a Java program native. All because of the vast number of mods that exist. And Dota now and then for playing with friends.

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.

Right now I'm really getting into old school games or games that have the old school look. Here's a few which have native Linux support:

• Stardew Valley
• Broforce
• Carrion
• Dusk
• FTL: Faster Than Light
• Huntdown

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!