Well, I've played for a couple of weeks now, gotten the feel of the game and all and thus have ended up with a point which I feel is rather important.
I think that the game is way over the top when it comes to the amount of mouse clicking that you have to do, and is more or less an invitation to RSI regardless of whether you take regular breaks or not. It also is a huge amount of unnecessary requests being made to the game server. A good design uses as few commands/clicks as possible and is a mentality which should never be ignored. The number of mouse related actions have to be reduced for many instances in this game, like farming or moving/dropping items. Pathfinding is also a must for characters, to remove the need for excessive manual navigation when it's not needed, and eliminating even more needless clicking. The seed sorting feature is a life saver, as it eliminates a huge amount of clicking, but I feel it could be improved even further. Most ideal would simply have a "sort" button or something which sorts everything in your inventory, including seedbags in one fell swoop.
For farming, it would be ideal if you could simply designate an area you want to harvest or plant (maybe get a menu of some sort if you have multiple seeds) and let the rest be automated. For picking up/dropping items, selecting groups of items at once is also a must. Construction like fences can also be simplified by using the standard approach of choosing beforehand the length of the fence and then automate it.
When it comes to ranged combat, the target that is designated should stay designated, but at the same time be able to designate another target with a single click. I have not dabbled much with the melee side, but I did notice that there were cases there where you once again had to re-designate a target when using a move.
I'm sure there are even more areas which could be slimmed down clicking-wise, so feel free to add any points that may have been missed.