what a great game! Played through the LD49 version today, and half of this expanded version (will come back and finish soon!)
I could see this being a hit phone puzzler! Doubly so If you could find a way to somehow procedurally generate levels so you could have a sort of "Endless" mode, or maybe a "Puzzle of the Day/week" sort of a thing where people could try to get on a leader board based on how quickly they cleared it. Or even a Puzzle creator so that Users could generate content to keep people engaged.
Things to think about that could create more puzzles:
1. atoms that could "Catch" stray electrons (I'm thinking some indicator on the "Proton" that says how many it can hold, after which it would pop like normal.)
2. atoms with state changes (I'm thinking of things like the red + switching to red x every other Action, or Yellows that rotate 1 direction clockwise per action, et al... )
3. Electrons of different sizes that travel at different speeds
4. Some sort of "Shield" that absorbs X amount of electrons before opening to the atom below
5. moveable atoms that could be combined into new shapes (a yellow pointing Up and a yellow pointing down combine to make a blue that has both, et al...
6. inactive "Neutrons" that when an electron passes through their space change their direction
I say all of this just to encourage you, as i think the game is great and would love to see more of it! but even if this is all i ever get of it, i was very happy to have played it!