SAF was a manager that put a lot of thought into his backroom staff. Throughout his time at United he always had a good number two (Brian Kidd, Steve McClaren, Walter Smith, Carlos Queiroz etc) I find it hard to believe that he would've kept Phelan around for so long if he didn't rate him. Make no mistake Phelan played an important role in that set up especially in Fergie's later years when he was getting older. There were a lot of times when Phelan would be the one out on the touchline shouting instructions.
Also, Rio said on his show a few weeks ago that Phelan wasn't involved too much in the day to day training and it was Rene that did most of the coaching. Of course Phelan was involved in tactics and team selections but come on SAF was calling all the shots. It's hard to blame Phelan for us playing 'pragmatic football'