Thank you for your comment, it is very helpfull.
Procedural generation for this game isn't easy. A single misplaced atom can ruin an entire level. I may try it if I decide to turn this game into a bigger project, but I am not here yet.
I will release it as it is (on mobile app stores and browser games websites) and see if the players want more of it.
Your mecanics suggestion are noted. Especially the "2" one. I though of manually rotated atoms, but atoms that rotate by themselves have a lot of potential indeed.