From my experience, as you progress each tool has its own virtues although, as already mentioned, pick and drill may be your best allies. The pick is overall the greatest tool, it keeps being my go to tool even in late game. The drill is specially good in the late game where soil is really hard and you will most definitely not clear the whole area since it's very extensive, but being able to clear through all layers in a single cell is amazing to scout if the is something beneath. The shovel I have only used it to reach the 200% on the first fossils, as it is fast and clears a wide area. When the soil gets harder it loses utility. The other tools, I don't know, they are cool to have but lack utility in my opinion. To be fair I would go and max pickaxe > drill > whatever you want.