I've only discovered this game for like a week, but I'm seriously hooked!
Only complaints that I have is that the icons for the planet types in the research menu tooltips are hard to tell what planet type they are. It's also generally more difficult to distinguish xeno planets from jungle planets. Maybe make the xeno planets purple to help distinguish them from jungle planets and earth-like planets?
Also, it'd be great if you had some kind of guide or wiki to keep track of what structures we can build on what types of planets, and also distinguishing which structures can be built on which planets with which upgrade.
And like other people have said, an endless mode, or maybe a sandbox mode, would be amazing for this game!
Another thing, although this is less about general game design, it makes me kinda sad that you're moving this project to 3D. You have all this beautiful pixel art and animation, so going to 3D feels like putting it to waste. But I'm not discouraging you from going to 3D if you think it makes the game better. I understand it's your game, and you're free to make it however it pleases you.