This is super cool! As a chem minor, I think this game would make for a fun introductory to basic covalent bonding for younger kids. The visuals are great, (I love how the atoms are little bean dudes) the gameplay is fun, I dig it! Forming methane has never been so fun :)
Another compounds that I think could fit in this game would be ammonia (NH3), which would work as a lower difficulty carbon. (carbon makes four bonds, nitrogen just wants three)
The last level was quite hard! The ethane was so tough, I don't even want to think about forming a higher level alkane.
Also, I was thinking about how big you made carbon - it'd be funny to see a heavier element on this scale. I could totally imagine a final level with a massive atom. (Like, uranium would be gigantic)
Wonder if there's some way you could incorporate double and triple bonding? That'd be cool. You could also make the atoms repel each other - which would make it easier to navigate/less chaotic, and more educational.
I wonder how you could incorporate electrons? I think if you reduced the stretchiness of the tethers, and made the scientist pull one electron away from one of the big atoms, and shoot it at the small atom, which then binds the two together in a buzzing yellow electron cloud, that'd be cool. The tethers could have a minimum and maximum length to make the atoms actually maintain a structure. But I get you're sort of going for a simpler look.
I really like this game! I often work at stem summer camps, maybe I'll convince the camp directors to let the kids play it :)