Huh -- expertise! I have a lot of opinions.
Played the download version and found it easier to work. I was still usually lost though and never could find features that I know are supposed to be there. One thing happened in both plays that seemed weird: Fairly early I came (I think) to a hadron tree; shook it... and was then surrounded not by protons and neutrons but by He nuclei (as I recall...). That points to a bigger issue, that this is a game about particle physics without any physics. I acknowledge that mixing "realistic" scales and velocities and whatnot would be... tricky... and modeling interactions in this particle menagerie would be crazy. Just the same, it seems odd that electrons are wandering around among all these bare nuclei without organizing, and collecting loose individual quarks is *opposite* physics. I don't know what you do about this.
Another way to put it is that I've spent a couple hours with this, amassed maybe 180 types -- so just scratched the surface -- and my relationship to pions is the same as it's always been: I've heard of pions but don't know what the point of them is. What you've got here is attractive and partly great -- a game with a nuclides chart! -- and partly misses. From the point I've gotten to it would be hard for me to learn any more because I can't really do anything on purpose with my inventory, which itself has been collected mostly at random. Crafting is fun, but I've got 56 recipes (and where did I get them from again...? Are there more?), have done 40, and don't know how to get the pieces for the others. It would be dumb to shoehorn a quests mechanism or anything like that into this, but maybe a bit more causality would help organize the experience.