After you get every upgrade in the game and beat both bosses, there really is no incentive to keep playing. I understand that there is no one basic solution for this but I believe there might be somethings that could help the game. For example, something like a leaderboard system could encourage hardcore perfectionists to try and get as high on the leaderboard as they can. Or maybe, and this is asking for a lot here, have an online 1v1 system, where you could see who can get the most points in a certain time frame.
Of course I'm not a game developer so anything you come up with will probably be better than my ideas.