Spawners: Oh! Yes, I see that now, it's spawning the yellow circle. I was reading the "color change" as "capturing" the spawner, especially since my score was going down... that made me think my score was just the total number of spawners I had "captured." I should have realized I wasn't actually "holding" 20 separate spawners at once, though!
I guess I was thinking of a virus, taking over a cell to make more virus instead of more cells... so I was expecting that the "spawners" were the ones making the antibodies, and that capturing them might (in some later version of the game) allow you to have it make more of you instead. Thinking about it more, maybe "capturing spawners" could determine how quickly some kind of "viral load" bar progresses? So when one "flips back," it's not a total reset. Just an idea!
Expanding pathways: My idea there was that any new pathway opened would be permanently opened, even if your score decreased afterwards! Maybe it opens the second you hit the threshold, or maybe you have to arrive at the barrier with the correct score to break it down. The better you play, the more quickly you can hit the next threshold and move onto a more efficient loop. (But that's my bias for games where routing/refining is involved.)
Map: Since you mentioned the "you feel small in a large space" feeling, I think that's a good point and a good feeling to try to capture! And yeah, just having a nice map/mini-map of the area may detract from it. What about a button that lets you zoom way far out? That could help showcase how small you are, maybe? A persistent mini-map might end up trivializing the exploration / learning aspect of the game... whereas being able to get a glimpse of the larger surrounding area might help a player who's willing to spend the time zooming out get a sense of how everything fits together?
I'm glad you found my comments useful!! I hope you find mechanics that you're really happy with!!