Out of all 3 of them Naismith is a more natural "box" player.
He also isn't as good as the other two outside the box.
Mirallas and Barkley in their natural positions with Naismith up front keeps us strong in 2 positions - playing the others as a striker means we could be strong in only 1.
I think Osman or Pienaar down the middle would keep us strong in the middle too.
I guess at the core it comes down to a few things:
I think Barkley is talented enough to adapt.
Out of the two Barkley/Naismith I'd rather have Barkley on the pitch (not meant to be a dig at Naismith, I still think he'd be used later as a sub).
Barkley would control and distribute the ball better, even with his back to goal as he comfortable making space for himself.
Naismith is the closest thing we have to a Cahill these days, but he's just missing a little of that same threat and nuisance ability that Cahill had which allowed him to play as the furthest one up the pitch when we had our annual striker crisis.