I looked over the topics and didn't see suggestions so I'm not sure if this has previously been suggested. I'm sorry if it has.
My idea is that since it takes pet points to garden, perhaps mini games to refill it would be helpful since after I'm done killing bugs etc I have no points left to level my pets.
The other idea is that perhaps if no mini game or bubbles are possible, perhaps using mana for gardening or creating a type of plant mana all it's own would help those would be gardeners out there
The idea is that kingsisle needs to make money that you can refill your energy using crowns. As most things in game cost money you will come to realise that it can be disheartening sometimes. I doubt they would change existing system. Just try to plan your gardening well!
I recently started the game and gardening & crafting. (BEGINNER) I jump on for a short bit in the morning to do mini games with pet. I do my gardening in evening. I have only 8 plants at this time.