Thanks for these great suggestions. I did actually update the game to remove the quest pop ups and a small notification is shown instead, is this not showing for you? The quest complete popups are still there however, maybe I can apply the same kind of system but with a small text summary showing what the rewards are. A list of recently completed quests would also be a good addition. I have added these to the top of my to do list.
The mini games will become harder and take longer as the player progresses, at the moment they are not balanced. The idea is that you need to keep upgrading levels and various features and research to progress so there will be blockers at some point. More mini games will also be added with more interesting and more complicated mechanics.