More seed boxes! Or at least a Mac version of VST. I really need a VST for Mac, for my PC savegame data transfer (my seeds are all locked up in the .vst file).
More plants, more spaces to grow plants.
What's with the umbrella in the lower left corner of the nursery??
New customer thought bubbles.
Multiplayer mode - buy seeds/plants from other players, or sell your seeds/plants to other players.
Special stuff in the shop to make your cheap water last longer if you cannot afford the good stuff. And same with the soil (for instance, you have mostly cheap plants but stumbled upon a magic plant, buy some stuff to make your soil temporarily better).
A button to harvest all seeds.
More realistic pricing for extinct seeds. $2000? c'mon people.

And one more thing: PT for Mac has an annoying problem.. when I am selling stuff in Nursery, I have to keep the PT window forward all the time, so I can't do other stuff - I mostly end up walking away from my Mac while the plants sell. A fix for this would be great.