Im not entirely a fan of my axe/hammer/etc being tied to a single contextual button that you press and hold. I believe it would be better if the Omni Tool took a single item slot (maybe add a Tool slot). Once equipped it would function the same way the axes and hammers did in the first game (swinging with mouse click/ RT on Xbox controller). The contextual use can stay as it would pick the appropriate tool depending on what your looking at.
The press and hold functionality that exists currently leaves a lot of error, especially if there are many resources near each other. You also tend to be interrupted if your buggy passes through your crosshair in third person.