Yep, agree with pretty much all of that.
The issue has never been playing Yaya in a two man midfield, in and of itself. Even this season, the majority of our best football, with the exception of Sevilla, has come when he has played there. The problem has been that we haven't been anywhere near compact enough for the majority of the season, notably because Kompany hasn't been playing. It's not the only reason, but it's a huge one. First five games, we defended aggressively up the pitch, compressed the game, and there was no issue with playing Yaya and Fernandinho together as a two man midfield. Kompany gets injured, and suddenly our back four are defending 10 yards deeper, meaning that there's a huge gap behind the midfield, and Yaya looks hopeless as any semi-decent opponents are able to get into that space so easily and hurt us. Kompany comes back, we start defending aggressvely (properly, you might call it), and Yaya looks entirely comfortable again playing in a two man midfield.
He's obviously not the player he was in 2011/12 when he was at his peak. But if Kompany stays fit until the end of the season, he'll still have plenty to contribute.
And I share your hope that Pellegrini sticks with the same system from hereon in!