It's telling that of all the objectively better, more expensive, more complex space games I've played since my middle school years... Escape Velocity still ranks #1 in terms of sheer joy.

It feels a lot like Populous: more fun than the sum of its parts, and only explicable as tapping some Miyamotoesque yearning in the zeitgeist.

Yeah, definitely. I think a lot of that for me was that the universe felt very alive - ships coming and going from planets, comms, recurring characters. I haven't found anything quite like it since, though Starsector comes close in some ways (and is extremely good in its own way, you should check it out if you haven't).