I personally love Naev and Mindustry
Mine would be Thrive, not so much due to its current gameplay, though it is okay, but moreso due to an unwavering commitment to a vision. It has gone on for years and is essentially a scientifically close to accurate version of spore. They have almost finished the single cell stage and are working some on the transition to multicellular now as I understand it. I find it to be an impressive project as it started from the disappointment with spore and has evolved into something that I would genuinely suggest as a learning tool in middle school biology class.