Obviously Ferrari missed Massa scoring points in both championships, this is a fact. If Massa would have taked some points from From Red Bull or McLaren in some races he would have been really useful for, a: Help Fernando on his championship fight, b: Help Ferrari in the constructor champiosnhips.
Saying Ferrari prefeers him to be not competitive makes no sense at all.
Answering to your question. First season after the Hungary accident, he was recovering the pace possibly and getting used to the car again, it was really trayumatic and could have been even worse, Massa knows it. Massa psicollogyst told a monthy ago he was almost fully recovered... A MONTH AGO.
Secondly, Alonso always proved to be better setting the car up and making an average car as good as possible, or at least driving it to the car limits, so if the Ferrari was not the best of the cars, Massa was racing wherever he could do it, midfield you say. Otherwise, how you explain Massa being so competitive last part of last season and these two races of 2013 season? I agree with some copmments above saying Massa depends directly on the car performance.
Fernando always outpoaced his team mates in race pace historically, and beat that will be really hard for whoever is sharing the pit with him.