Pedro is a wing/inside forward, not a CF #9. Pedro can sub for Neymar in the current formation with little effect on the basic tactical formation, but obviously subbing Pedro for either Suarez or Messi changes the whole system. Obviously, no bench player could replace Messi, but a #9 sub could be useful, simply to be able to keep the same tactics when Suarez is subbed out. This is why I currently favor Sandro of Barça's available options, as he plays quite well with his back to goal and can keep the CBs occupied. And his short passing is actually better than either Suarez or Neymar.
The performance in the second half is less a reflection on Pedro than it is on Suarez and the system built around him playing centrally (and the nature of the tie at that point). The performance of all three forwards in the second half was 0 chances created, 1 shot, 0 goals.