You decide! I choose WSAD because most games use 'em, and it's best just to go with the flow. Jacob
With me it depends on what I am doing and for how long. I generally use the arrows but if I am farming chests in a repeatable pattern for any length of time my hand gets sore and I switch to WSAD to give my hand a break. I do tend to run into more walls that way as I am not very ambidextrous.
I use both but I would say that I use the WSAD more. Like others I like the fact that they are right next to the ship battle #s 1-4. I also prefer hitting the X to interact instead of double clicking because often I left click and hold and move the mouse for a different angle as my pirate runs around. But I definitely use the arrows as well.