spells should have a hotkey so you dont have to move the mouse a thousand miles to level them up, other then that great game, have to choose between crafting, leveling up, add more troops or adding skills, there is never enough money lol
i think you need to work on the heat exchangers, they shouldn't be able to blow up a generator, unless it blows them all up simultaneously, it should keep them at just under max if they start to retain heat, in my setup im using water cooling and i am limited by have 3 or 4 random generators blow up, but i have others that still have full water, meaning the ones full of water aren't getting enough heat, and the ones that blow up are getting too much.
don't know how to quote, sorry for leaving in a separate comment, i know that, but when all the molecules are popping on screen, there isn't really a way to determine if you have clicked on it or not, that's why i was thinking something visual as well, rather then relying on my memory.
when trying to find out what molecules you have already slicked can be difficut, maybe make them grey when you havent clicked on them, and then color them when you have, kinda like a discovery aspect of playing the game manually
 "Royal Heroes"){kind=icon}
 "Reactor idle"){kind=icon}
 "Idle Evolution"){kind=icon}
 "Reactor Incremental"){kind=icon}
 "Hack Slash Crawl"){kind=icon}
In config -> molecules you have a list with all molecules clicked and sold.