Its about the number of people you are fighting against. If your team mate is a designated number 2, that removes one driver from the equasion. For example, Hamilton would have to beat Alonso, Vettel and Button if McLaren run an equal driver policy. Beating Button would also mean beating him on raw skills and not though any car advantage. Removing Button means Hamilton would only have to beat Alonso and Vettel, and if different cars, its possible that could be easier if the McLaren is ahead.
But its not a perfect way to run a team. If you designate a number 1, and then they have some bad luck or don't perform, your chances of winnign are reduced. There is also the potentially difficult situation of your number 2 having a much better start to the season than the number 1.
But its all swings and roundabouts. Its 2 very different ways to run a team. McLaren are the equal team, Ferrari are the 1 man show, and RBR are on a sliding scale in the middle depending on how they are feeling at the time.
There is no right or wrong way, both have had success, but sunama is right in saying that more often than not, when the equal drivers tactic has worked, its been when the car has been the best by some margin (McLaren in the late 80's, Williams in the 90's, etc).
Having the best car and running a 1st driver policy is almost guaranteed to win you the championship (drivers at least), as shown by RBR this year.