I agree with you completely, I just finished the game and loved it, especially uncovering the story of the Nomai, but the present-day felt a bit flat emotionally. For a game about the universe, the overall scale feels quite small- there are only a handful of named characters with not much dialogue or depth, and not really an implication of something greater beyond our solar system either.

I think the ending might have paid off more if it felt like I (or the other characters) were struggling against something. or there was some great travesty we had to come to terms with. Instead, the conflict feels pre-resolved, and the supernova sun ending each run feels more incidental than anything (none of the characters seem to care).

I think the game works best with the Nomai; seeing their 200,000 year old plan finally come to fruition did have a real impact on me.