Things I'd like to see either in PT2 or updated in this one:

1) Being able to multitask while selling stuff in the Nursery. Having to wait and wait for that last plant to sell when you could be planting new plants or buying new supplies is rather irritating at times... Or at least having a table in the nursery that you could place x number of plants on that would continue to sell even while you weren't in the Nursery screen (could even take a certain amount off each plants' default selling price to make things more realistic/difficult).

2) Being able to view (and change) more than the asking price of a plant when clicked on it in the Nursery. I've had several times that a plant hasn't sold and hasn't sold and when I go back into the Greenhouse, I discover that it had gotten infested while I was trying to sell it. Being able to spray an infested plant in the Nursery or change that single plant's selling price without having to go back into the Greenhouse and then back to the Nursery would be a great benefit.

3) An easier way of moving seeds from the Seed Storage boxes to the pots. Right now you have to move the seeds from the Seed Storage box to the Seed Tray, switch back to the main Greenhouse screen, then move the seeds from the seed tray to the pots. And if you're planting all 15 pots you've got to make two "trips" to do it. Either making the Seed Tray the same number as you've got pots or being able to drag a seed from the Seed Storage box to the Main button on the bottom to automatically seed the next available pot. (Kinda like moving a seed from a plant to the Seed button on the bottom automatically places in to the Storage box only in reverse.)

4) A 'harvest all' or 'sell all' option for seeds so we don't all develope Carpel Tunnel moving each individual seed to either the Seed Tray/Box or Trash Can.

5) A zoom in and rotate feature for pruning (even if it's one single table in the Greenhouse that you've got to move each plant to to use it).

6) I'd like to see the Virtual Seed Tray incorporate into the game itself - or at least a basic version of it. And yes, I know it's easy to use VST (and I'm one who DOES use it) but as has been pointed out in that thread - it doesn't work on Macs and you've got to shut the game down every time you want to move seeds from the VST to any of your games (and if you're running multiple games at the same time - it can be aggravating to constantly do).
a) Say, having a Seed Storage House in addition to the Boxes but you can only have one type of each seed in the Storage House (that would let people keep their seeds for further cross-breeding later without making the game too easy having massive amounts of one type of seed at a time).
b) The suggestions of having an in game breeding chart are awesome - maybe one that keeps track of what seeds you've got and what any/all cross-breeding you've done to make them so you don't keep cross-breeding the same plants over and over and you don't have to kill a small forest keeping things straight on your desk.

7) A bigger Tool tray so you're not forced to choose between making your plants grow faster, getting more out of them, or keeping them healthy.

I'm pretty sure I could come up with more but I think those would help the game without making it too easy to really play anymore.