Well yes but:
1. It WAS only Northampton.
2. Against better teams his lack of mobility/pace will be exposed unless he is protected in a 3 man midfield, and even then I have severe reservations - Nevertheless imho we should try a Carrrick-Morgan-Pogba triplet (though I know how effective Herrera is I would like to see how these particular players combine).
I dont think Carrick's lack of mobility/pace would be much of a problem in a midfield 3 with Schneiderlin and Pogba. Carrick has never really been one to run around anyway. He positions himself to intercept the ball a lot of the time, so if he covers the space infront of the back 4 intercepting, that leaves Schneiderlin to do the running and closing down, with Carrick there to collect the second ball. Obviously Pogba would chip in with his fair share of defensive work, but having those two behind would allow him to get forward more into the areas hes most dangerous.
As far as the front 3 go its a bit more of a headache. I think to get the best out of the team, and not just fitting individuals into the line-up, I would go for one of Martial/Rashford on the left. Both have a similar game when playing from ther left. Both get the ball down and drive towards the box, committing defenders, then either taking them on the inside for a shot, or stay on the outside for a cross.
To balance that threat on the left, I would have somebody like Young on the right. Putting in quality crosses for Ibrahimovic to get on the end of, or for Martial/Rashford coming in on the back post. If you have Valencia at RB and Young at RW, you are guarentee'd a **** of a lot of work rate down that side. Both have the ability to cover for each other and also have the pace to get back when needed.
Obviously setting up that way leaves out Mata and Mkhitaryan. I really havent seen enough of Mkhitaryan to know if he would be any good on the right, playing in a way that ive said above for Young. Or if he has the work rate to match and get back defensively. So it depends how Jose wants to play it. I think the team would benefit more from a 4-3-3, with Carrick, Schneiderlin, Pogba and Young, Ibrahimovic, Martial/Rashford. But then your leaving out some of the big name players that he may be under pressure to use. If he persists with the 4-2-3-1 then he needs to get the balance right. First off getting Rooney out of the team. But again who do you leave out in that formation. Do you go Carrick, Schneiderlin in the 2 with Pogba as no 10? Or put Pogba in the 2 (so not getting the best out of him), to play Mata/Mkhitaryan at 10?
He needs to find out what he wants and fast. No good being like LVG's first season when he stumbled on his best formation/players in around February.