The club's all-time leading goalscorer, now manager at Derby County, expects his former side to finish outside the top four this season and predicts a three-year wait for their next Premier League title.
Rooney also questions the character and commitment of United's under-performing players, who are currently languishing in fifth place amid yet another disappointing campaign.
In a revealing interview, the 36-year-old told Drive: "I said it back in 2009 and 2010, losing Ronaldo and Tevez was a big loss. I still believe they've struggled to recover from that.
"Losing Alex Ferguson and David Gill was a big blow for them. Ed Woodward came in and I think Ed has done a good job.
"They've changed the manager a few times and they just need that stability and have some time to work with the players.
"Man United aren't going to win the league in the next two or three years. They need to use this time so in the next three or four years they are challenging again.
"They are a long way off it at the minute."
Asked whether United will qualify for the Champions League this term, Rooney added: "I think it's going to be tough, if I'm being honest. You can see confidence is low and there are other issues going on around the club.
"They've certainly got the players there and they have got some good results of late, but performances haven't been great, that has to improve.
"Them players need to show their character, show they're all together and fighting for that club - because there are games I have watched when you question that at times. That's me being honest."
He continued: "If it carries on going the way it's going, I don't think United will get top-four. I think there needs to be serious conversations among the players, without coaches and staff there.
"They need to come together, whether they're friends or they don't like each other, for 90 minutes they need to come together for that club."
When pressed on who he thinks will finish fourth, with Spurs, Arsenal and West Ham in close proximity, Rooney said: "Tottenham, I think they might sneak in there, they've got a very good manager.
"If it wasn't United, I'd like West Ham because I like David Moyes and I think he's doing a great job there."
Having won five Premier League titles, Rooney understands the level of expectation at Old Trafford, despite their barren run in the top flight since Sir Alex left nine years ago.
He suggests the Red Devils have lost their winning identity, but maintains hope they can return to former glory in the long-term future.
The Rams boss, who is doing a spectacular job under difficult circumstances at Pride Park, also hints that he wouldn't mind being part of that future.
"No it hasn't [felt like the Man United of old]," he added. "Man City and Liverpool over the last three or four years have taken it to another level.
"Two incredible teams who are enjoyable to watch and hard to catch. Manchester United as a club are more than capable of bridging that gap.
"The decisions at the end of the season, whether Rangnick stays or someone else comes, it has to be the right one."
When asked if he would take the job at Old Trafford, he said: "Everton and Manchester United are two clubs in the future that I would love to manage. I would love to go in there and challenge myself.
"They're two great clubs. I said a couple of weeks ago in the press conference, I'm doing a job at Derby and my focus has to be on that, because it's a day-to-day job that needs all of my attention to get the best out of myself and the players."