I think it was a combination of more things. Basically, Messi played vs Madrid in the exact same way like today, but because we didn't use a 3-4-3, we had a major hole down the right. And that whole was exactly where we should have insisted the most, on Marcelo's side. You could actually see Marcelo having no one to be concerned about, because Messi was playing in midfield almost all the time.
Another option would be to play 4-3-3, but with a 2-1 midfield, instead of 1-2. That 1 can be Messi, but when you use Messi in a midfield 3, you have to use 2 ball winners behind him. So, Mascherano - Busquets, Neymar - Messi - Rafinha, Suarez, can also work. It transforms into a 4-1-1 on defensive transition, with Neymar - Busi - Mascherano - Rafinha in midfield.