I think one of the biggest problems is that Fernandinho never actually steps up his game when playing alongside Fernando, he doesn't offer any more attacking than he does alongside Yaya, which pretty much defeats the point of playing Fernando alongside him. I'm always a bit surprised by this, as Fernandinho always looks to have more to his game than he's allowed to show when alongside Yaya as he has to play with the handbrake on, but then when he's given the chance to be more free he has never taken it. If you are going to play the two of them together then Fernandinho really needs to do a lot more attacking, while Fernando does his usual role, but for whatever reason that's never really happened.
The exact same could be levelled at Yaya when he starts in attacking midfield, he should produce more attacking play when he's moved forwards and had his defensive responsibilities taken off him, but he very rarely does.
If playing Fernando alongside Fernandinho and Yaya doesn't give you more attack from those two, then there is really very little point in doing it as you are just losing a number 10 and gaining a Fernando, which isn't much of a trade. You sort of gain a bit more defence as you have two midfielders who defend in the middle, but by having Yaya further forwards you lose any ability to press up the pitch as he simply doesn't do it. In a tough european game against a team who wants to pass it through the middle then I could see the point in the two Ferns together, but not with Yaya in front of them (like Roma last year when it was pretty much perfect). Other than that then I can only see the point in Fernando being backup to Fernandinho, to play alongside a more creative CM.