Some thoughts re:planting cuttings:
Instead of simply planting a cutting in the ground and rolling the dice (with terrible odds), make the player actually work for it.
Cuttings must first be nurtured in a planter for a couple growth stages before they can be replanted at their final location. Their base chance for survival as a cutting could be equal to the fertility of the soil placed in the planter (This requires adding some functionality to planters, but it's straightforward and adds a touch of realism, albeit to an object that, at least as of now, doesn't see much use).
While in the planter, the tree must be watered on a daily basis. Any stress the cutting/sapling experiences, such as failure to be watered or being subject to extreme temperatures, could potentially kill the plant, with the odds getting higher as consecutive days of stress go by. For a bit of extra complexity and realism, the cutting/sapling's tolerance for stress could gradually increase over time until it maxes out at the end of the first stage.
When the sapling is mature, which could be any point during the second stage of growth, the planter containing the sapling can be picked up like a skep, dropped into a 1x1 hole at the location you want the tree planted, and then shattered (the planter, that is) to finalize the process. (Open to other ways of that last substep, but what I have is functional).
Simple and straight forward, but still actual work. The same process could work for berry bushes, too. There's one little exploit that's easy to see right off the bat that involves digging out the tile immediately below the tree in order to retrieve the original higher quality soil in order to reuse it, but there are ways around that (Downgrading the soil underneath the tree to medium if it was originally something higher, or for a move involved and realistic solution, introducing a rudimentary root system that would stabilize nearby soil and prevent it from being dug up).
Hell, you could even keep in the current method for planting cuttings in addition to the above, they'd just have a much lower rate of survival than ones that are properly taken care of. There's also the thought of modifying it so that the base chance is (soil fertility)/2, which would keep the status quo when a cutting is planted on medium fertility soil.