Yup, abilities, items and other actions are animated using Battle Events (and you can use them to do much more with them than the settings allow).
But why do you need to use a Wait for Input step in your event? The control map handles the input and calls the ability - the battle event will animate the ability. The target selection will be gone if you enable Use Auto Target in your control map's key.
Or, e.g. when using damage dealers/zones for doing damage, you can set the ability's target range to None to not require a target and simply damage whatever is hit (see the real time battle game tutorials for more details).
Mecanim's Apply Root Motion can't be used with character controllers, the rest should be working fine.