They're about equal defensively, although Gilberto shades it in the air, but Makelele was the better ball player. Makelele was known as the player who just sat back and played 5 yard passes but he was much more than that, watch him closely when pressed, he always played himself out of trouble in a similar way Xavi does. He was actually the player who started off most of Chelsea's attack, teams only picked up on this later and they put players on him to disrupt Chelsea's build up play.
I remember him being France's best player on the pitch in their defeat to Spain in 2000/2001, and he was playing out wide(on the right, played there for Nantes btw).
There was also that amazing 40 yard outside of the foot pass with his weaker foot in France's boring 0-0 opener in Euro 2008(think it should be on youtube as it was France's only chance in the match).
Gilberto never pulled off stuff like that.