We created chances and we should have been out of sight quite early in the game. That's one way to look at it, especially when you consider that Stoke haven't shown anything thus far in the season. But there's also another way to look at it...
The biggest problem this team has is that it finds it very difficult to raise the tempo of games and play on the front foot for two or three periods of 15-20 minutes during a game in order to pin down the opposition and subsequently find goals through rhythm. The absence of a tempo setter in the midfield is more than evident but things become even more difficult by the lack of wide players who can unbalance compact defenses with their 1v1 skills. Rahsford does the best he can but he's very young, he lacks experience and has the usual blips in form even through the 90 minutes of a game. The result of all this is that most of the time we try to pass our way to a clear cut chance which isn't really our forte. And the fact that Mourinho is a speed merchant, he creates sides which are lethal on the counter, complicates things even more. Fergie had Carrick in his prime and, moreover, he was willing to overuse the long diagonal in order to get the early cross in the box. Jose likes to go through the middle more... his team, his tactics, his responsibility to work it out.
Another issue is the #10 role. Rooney deserves all the stick he gets on this forum but games like this one (and against Zorya) when we face 10 men behind the ball defending in avery compact shape show that Mata isn't a good fit for the position either. Where we need a play maker who is good in tight areas in order to find pockets of space in between the lines, who will try to link up with the other attackers and spot opportunities for late runs in the box, we have a player who moves as far (deep or wide) as he can from his teammates just to find enough space and time on the ball that will allow him to turn and raise his head in order to see his options. Having Zlatan in the same team dropping deeper doesn't help either.
Third point, very little off the ball movement in the attacking half of the pitch. Some good moves from Zlatan but today we mostly relied on Lingard's diagonal movenet in the half zones to create decent overloads. Other than that, we were rather predictable: Zlatan will drop deep and this will force Mata to go beyond him and try to stretch the defense but Mata is no threat for big CBs, so that's an less option. Rashford/Martial will hug the touchline and wait to get on the ball and take on defenders while Pogba is the only threat from the midfield. Valencia isn't considered a serious threat by anyone in English football anymore and Blind can cross the ball from the left but if you put the opposition's best creative/attacking player on his side you can count on him staying deep because he lacks pace to track back his man from a very advanced position. That's about it.
Mourinho said that his aim isn't to create a defensive wall at OT. That's good to know but the teams he deploys are ones who are willing to take considerable defensive risks that don't pay off as often as we would like. But if he leaves the same spaces open in between our lines at Anfield, we are going to get annihilated.