It may be convenient
but I can also see it getting people into trouble
ex:
there is fire on the ground like in your picture. User uses waypoint system to plot a safe course around the fire. Clicks to execute move. Character begins moving, once it reaches the first waypoint your character spots a trap. Keeps moving... walks into trap. Boom! Dead.
Avoidable if you were moving each step manually.
I don't see the point. The very same thing happens when you give your character the order to walk in a straight line. That has nothing to do with waypoints actually.
And this could of course be avoided by a simple mechanism that lets you choose to interrupt your move once you spot a trap.