His best position is behind the striker. He needs a player that can pin the CB's back. Pep noticed this back in 2011, he played Villa in front of Messi with Alves in charge of the entire right flank in the CL final.
In 2012, Messi was playing behind Alexis or Cesc, with Cuenca/Tello/Pedro keeping width and Alves in charge of the right flank.
Our comeback against Milan saw Messi play behind Villa and Alves in charge of the right flank.
Against Apoel and now today he played behind Suarez and he was very effective. When Sabella asked Pep how he could get the best out of Messi, Pep replied by saying play him in the hole behind the striker. He gets more space and he can use those quick 1-2 combinations.
Since Alves has declined physically he can't really go up and down the touchline as used to. That's why I think we should move to a 3-3-3-1 with Adama in charge of the right flank, due to the transfer ban.