I've said elsewhere that Fred has all the requisite technique and intelligence that he needs. What he lacks is the strength to make it count under physical pressure. At this point in his United career, it would make sense to put him on a dedicated stength training program.
I have nothing concrete to back this up. But if the United coachng staff concur, that would explain his absence from the starting XI and only occasional appearances on the bench. It's not that he isn't a better option than Pereira (he's superior in every way, imo). It's that he needs the rest. It's easy to forget that players need recovery time from activities taken away from the pitch.
If Fred were deemed 'not good enough', he'd have been frozen out like Fellaini. Instead, he's being kept to one side much like Lukaku over the last few weeks.
It looks likes Romelu has been on a weight loss program recently. You can see it by the fact his energy levels were lower than usual (hence even less running than normal) and the obvious changes in his physique. The last few weeks have seen him return to his old self. An extracurricular gym regimen for Fred looks reasonably likely, considering we've only just witnessed it being used on another player.
On the other hand, maybe the coaching staff just don't think he's good enough. However, I personally don't see that as being the case given the obvious talent he possesses.
If I were a betting man, I'd put money on also Fred being asked to dedicate his time to physical development in the short term.