I was not expecting such a deep analysis for my question aha. You've given this game a lot of thought.
I like the idea of flower power and think it can help with progress by powering other resources or equipment...maybe something that gives you a perma-unlock or powers equipment.
As a game that appreciates all plants it is important that the progress system does not dictate which plants you should use (strategy is important but gardening is more fun!) using plant coverage to make power will be a great way to let you choose what you want by filling it with your favourite colours and plants.
Even a simple level flow like having a door to the next level requiring so much flower power to open will give you an overall goal in that area.
I am sure you have much richer ideas than the above. Your ideas on the game sound great and you have a much greater grip on it than I have :)
Appreciated the insightful response :)