If you hold X to bring up the command wheel there is the option to “Hold Here” this is the new “Stop” command. You can only use it with the command wheel though. Double -tapping X is now “Return” and triple-tapping has become “Flee”.

Edit: Another that sucks is that LT now “Takes All” from crafting stations instead of turning them on and off. You now have to HOLD LT to start crafting stations.