It likely won't ever be a drop-in replacement because a lot of X operations don't really make sense in Wayland. (Even in X, xdotool isn't perfect and a lot of its commands won't work if your window manager doesn't support the right hints) Unless you feel like volunteering to make a standard for this, you'll get the best mileage out of using an API specific to your compositor rather than waiting for someone else to come up with a standard. I know GNOME exports its internals with a javascript interface, and Sway has a way to run various commands using a JSON interface too.