I agree that the need for compost/crop dust should decrease the disease and increase the yield. In reality, when you use compost you increase your chances at having a larger plant with a greater yield than one using just dirt. Crop dusting is to prevent/treat disease, so logic would prove that if you use crop dust, you would have no disease.
The timing is very bothersome. I agree that the yield should greatly increase for the time spent on the node.
As for tending more than one crop. I have this down to a science. I will prep a node (compost, crop dust, scarecrow, then seeds) and not water it. I will then go to a second node and do the same sans watering as well. Return to the first crop, water, prune for disease, rewater, prune again, and then harvest. I will then prep that node again, turn around and water/prune/water/prune/harvest the other node. I keep this rotation going until I have the desired amount of crops or reached my goal. True, that is a LOT, but it allows me to manage more than one crop at a time and still get the best chance at a perfect crop.
However, I still can not tend to more than two crops at a time without risking losing one crop completely due to the timer.
It would make farming more fun to either decrease the animation time greatly OR increase the yield greatly.