Ways i see this working:
Most simply
Ideally - i have a feeling getting it to look like this would be very difficult, but the garden in the first scene is a good representation.
These are different techniques. The first one is a set of 2D pictures (think PNG files made with a pixel editor, or a paint program), where you program to blit images at the right position. Even your "ages of empire" dimetric screen is that. It looks 3D-ish, but it's just flat PNGs with a weird shape. Obviously, dimetric view gives bigger challenges in rendering and position calculations.
Your "Ideally" is a 3D world. You use software like 3Dmax or Blender, which results in a 3D model, which you then dump onto your video card to render. (At least, that's what I know. I have never done anything 3D yet, firmly stuck in the 2D dimetric, and hexagon worlds :p )
As for assets, read the pinned articles in the "Visual arts" forums, there is a list of publically available free art sets/sites there. You should check the license of a set before use, to avoid surprises.
What i am inexperienced with is the "game" aspect... how i can visually simulate this.
The technical term for the thing you are looking for is the model-view-controller pattern. While it's useful to read it, it's so abstract that you probably won't get much wiser from its description.
To make it more concrete:
You need a model, a world like a (2D) grid with vegetables, just think a 2d array of Vegetable objects. Each object contains the information of the plant at its position, amount of water, age, how much sun it got, did you talk enough to it, etc, just everything relevant to the game.
Next, you need a view. You want to display that world to the user. Build code that can draw some graphics (eg select a PNG image) based on the Vegetable object, and draw the selected image at the spot of the vegetable, to the screen.
Do that for the entire 2D array, and you have an area filled with vegetables.
Now, since the renderer only uses the Vegetable object data, and nothing else, changing a vegetable is easy. Just change the Vegatable object, and ask the screen to redraw that vegetable. Done!
The "changing" part is the controller, pieces of code that change the data, eg after time has passed.
A user interacts with the screen, and clicks at something. The controller receives the click, and performs the action in the world. It asks for a redraw, and done!
Of course it all sounds very simple in the few lines that I write, reality will be harder :)
But I think this is the direction that will work.
I haven't looked at your Unity links, as I don't know it. I do know it's quite good at 3D modeled graphics. If you aim for 2D PNG images instead, you may not need such a tool (but I don't know for sure.)