I agree with the stacking seeds of the same type on top of each other in your seed boxes

Also, having a storage house for plants old enough to sell so you can grow more instead of having to wait for some to sell.

Customer bargaining with you about the price of your plants would be a plus

As well as a "bell" or something to let your customers know you're closing so they won't keep standing around and you think they're going to buy something. Allow enough time though that if they decide they want to make a final purchase before the nursery closes they can do so.

There should also be some kind of loud "ding" to let you know you've sold a plant even when your PT window is minimized or running in the background.

You should be able to sell your bugs from your collection as well.. especially if you're low on money and really need something

Another good idea would be to make the tools section larger so you would be able to store more chemicals and whatnot so you don't have to run back and forth to the supply store or have to worry if you'll have enough money when that chemical is needed badly.