Most teams double up on Pepe because he's so dangerous with a free run. The problem is we don't have anyone next to him to make it count for anything.
The change Arteta made won us the game, it was also due to the execution of a great team goal and a solo effort. Once our momentum slowed, we were immediately vulnerable. Even though Willian went to the middle, he couldn't do anything to keep the ball or release pressure.
I think it was far less the shape that affected the game, and far more the change of shape that destabilized them and let us get in for a few minutes, and we made it count. I'm totally unconvinced that we can start that way and get away with it in the majority of games, if any at all.