Except to change the inputs from your TV to your Apple TV.
I still like the physical buttons on the remote better, especially for channel surfing, Guide info and muting or volume adjustments. If the iPhone goes to sleep, you have to enter your password and look at the screen to make any selection. Kind of a hassle (Touch ID would simplify it if you have that). No look, no login is better in my opinion. I personally only used Remote app once to test it when it first came out so I'm just speculating on the awkwardness of the operation. I don't use it.
It's a matter of taste I suppose, but it sounds a bit like what Blackberry users used to say.
I can't use dedicated remotes wether it's IR or BT, I need to be able to control all my equipment and don't want to use several remotes. I now use Roomie Remote; works great and will work even better if the next Apple TV would sport IP control.