That should be it. In a nutshell:
United's facilities are more highly-rated in-game than IRL public sentiment/results suggest
United's board expectations do not reflect the Glazers' IRL priorities, and are an idealized version of what the fanbase would like
United's coaching, scouting and developmental staff are overrated compared to IRL results over the last five-plus years
United's youth setup is overrated compared to IRL results
I bolded the one that I think is most important. The United board in-game places an extremely high priority on internal youth development and maintenance of excellent facilities. Since Alex Ferguson left, though, United has been more likely to prioritize signing high-reputation players, even at the cost of destabilizing the team and system.
Plus, I have a long-standing belief that the largest weakness of FM as a sports simulator (and I don't blame them at all, no one does this right) is that it is very bad at modeling bad governance and bad corporate culture. Man United should be highly successful. One of the reasons they're not is that their ownership uses the club as a bank, and the whole sporting hierarchy has devolved as a result. FM isn't set up to deal with any of that. It can only sim United's results as any club that has infinite money, good-to-great facilities and a sterling reputation, so United does well, just like every other club with similar resources and reputation does well.