On the other hand, if they introduce this system alongside the standard controller, it could be very helpful for some people.
For instance, I'd never (ever) use a smartphone over a controller, assuming one was available. On the other hand, I only own two controller for me and my partner.
We rarely need more than two, but there are instances where friends pop down, and we think "If we had two more controllers we could have 4 player coop"
This idea would then allow them to whip out their phones and tablets (or whatever) and jump into our game, without me having two extra controllers that hardly get used, and without them having to bring controllers with them all the while.
If implemented as a backup controller system, it's actually a good idea. Even if they charge for the app, it'd probably still be worth having it, if a controller breaks or the battery dies, you're not screwed - just get your phone out.
It'd be awkward to play with, sure. But it's better than not being able to join at all.