Alex Ferguson played the formation for which he had the ammo. It was good of him to break the traditional 4-4-2 and instead go for a more attacking 4-3-3, but he was done with the lack of sharpness in front of goal and some mediocre central midfield play. Even a team like Everton who complete out of the top four have a decent central midfielder who can win balls and control possession. It is high time United go after some quality playmaker rather than sticking season after season with Michael Carrick.
Felliani and Jagielka treated him like a school kid and also made sure their strikers were supplied well. All top teams have highly creative players in this position. Paul Scholes was good in his prime, but Sir Alex has to realize that this cannot continue forever. Shinji Kagawa was the only promising player who continuously tried to innovate things at the midfield.
Wayne Rooney was a pale shadow of himself and was too casual in his approach. You cannot blame Robin Van Persie as there was too little time and too little support. Also using Valencia in defense and keeping out Da Silva was a bad move. You can try your permutations and combinations during your pre-season matches, but you should never take any opponents in the Premiership lightly. This was evident in the Manchester City vs Southampton match. A small slip up and none of the teams are quite forgiving here.
United should not go back to the safe 4-4-2, a formation they are so used to as this only works in the Premiership. While you face teams like Barcelona, Real Madrid who more or less use the 4-3-3 with some variations, you cannot afford to rest all your attack on the flanks as most of the play is controlled form the centre. If Man United have to come with a serious challenge in the Champions League, they need someone like Xavi, Iniesta or Oezil in the position currently held by Carrick and as none of these players are going to be available it is up to United to pull an ace.