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

Kerbal Space Program!

Removed by mod

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

0ad, Wesnoth, Endless Sky, Mindustry

Damn so many great ones to choose from. I am big fan of Paradox strategy games, kinda in that order: Stellaris, Hearts of iron IV and Europa Universalis IV.

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!