So recently I just finished my plant journal, and since then a lot of the charm of the game has kind of worn off since the element of actively managing my garden is almost completely removed. A solution I have come up for this is the idea of the Undergarden, which is another plot the the player unlocks after finishing reaching [add number here] unique plants. The undergarden cannot support normal plant life, but has its own collection of plants that can be purchased using tokens. You start with zero tokens, and they can be bought for 1T overworld money. The undergarden plants produce token when sold, resulting in it being effectively separate from the overgarden, besides the purchase of tokens. Early game in the undergarden is incredibly slow compared to the overgarden, with most plants taking multiple days to harvest. This creates a transition period, where you still need to subsidize your token output with overgarden cash, so that the transition is less abrupt.
The main appeal of this idea is that it allows for end game overgarden to still exist semi independently, while also allowing for introduction of a significant number of meaningful new plants and mechanics.