The Phils had won five consecutive National League East titles and breezed to an MLB-best 102 victories in 2011, and because of their pitching, they were a lukewarm favorite to win the division again.
In the spring, the 68-year-old Manuel, the most successful skipper in Phillies history, openly talked about how difficult it would be to stay on top. Many refused to listen.
Obviously, Manuel's concerns were legitimate.
Barring a run reminiscent of the 2011 Cardinals, there will be no postseason and no sixth consecutive division title this year.
Instead, Philadelphia has struggled, and the team has been one of the NL's biggest disappointments.
The Phils raised the white flag before -- and after -- the July 31 non-waiver Trade Deadline when they sent Shane Victorino, Hunter Pence and Joe Blanton packing. They're using the remaining days of 2012 to "audition" players who might help them return to contention next season.
But with Utley and Howard back, they've played much better since their deals.
During an extensive interview with MLB.com at Citizens Bank Park the other day, Manuel was candid about what went wrong. For him, unless the Phillies have a strong final five weeks, he'll risk having his first losing season since taking over in 2005.
"When you win five division titles and have the best record in Major League Baseball, [the players] might take it for granted," Manuel said. "They forget the effort and the work they put into winning. It's hard for them to realize what goes into it, because they start thinking how good we are.
"They feel like they can turn it on and off whenever they want. They're getting older, doing less work and maybe aren't as hungry. If you slip some and forget about what it takes, that makes it harder."
For much of the first half of the season, the Phils played horrible baseball. Manuel agrees.
Aces Roy Halladay and Cliff Lee were pitching poorly, the usual sound defense was inconsistent, and without Utley and Howard, the offense sputtered. The bullpen, except for closer Jonathan Papelbon, was atrocious. Only veteran left-hander Cole Hamels (14-6, 2.99 ERA) and catcher Carlos Ruiz (.335, 14 homers, 58 RBIs) have had outstanding seasons.
To add to the team's woes this season, the Phillies' string of 257 consecutive sellouts at Citizens Bank Park ended on Aug. 6.
At the All-Star break, the Phils were 37-50 and mired in last place, 14 games behind Washington.
But Philadelphia has posted a record of 23-17 since then, and has climbed to third place behind the Nationals and the second-place Braves. The Phillies just completed a three-game sweep of Washington after winning two of three from Cincinnati, and the team has moved to just six games under .500.
Fastball down the middle: Analyze the season, Charlie.
"It's hard for me to sit down and make excuses," Manuel said, "but coming out of Spring Training, we knew we didn't have Utley and Howard, the middle of our batting order was gone, our big run producers. I knew offensively, that was going to hurt us tremendously, and when I looked at our bullpen, I saw a big question mark. We were depending on Chad Qualls and Jose Contreras. Contreras went down real early, and Qualls had a hard time helping us in the eighth inning. Antonio Bastardo has been trying to find [effectiveness] since the end of last year.
"Once our bullpen got exposed and we just didn't have very much power ... we started losing. To win, we had to steal bases, manufacture runs, but from a small-ball standpoint, we couldn't do it, because except for Jimmy Rollins and Victorino, we didn't have a lot of speed. No question, we were lacking a lot of offense."
Manuel points out that when Halladay was disabled with a shoulder strain on May 29, his team was a game over .500 at 26-25.
"We always thought if we played .500 baseball or a little bit better until the All-Star Game, we'd be fine the second half," Manuel said. "It didn't work out that way."
Halladay, the 2010 NL Cy Young Award winner, was out until July 17. It has taken him most of the time since then to build up arm strength and improve his command. Halladay is now 8-7 with a 3.88 ERA.
"I think he's on the right track now and will finish the year strong," said Manuel, who admits he's had trouble sleeping many nights during this season. "Cliff Lee is having a difficult year to explain. In my 50 years in baseball, I haven't seen a pitcher go through what he has.
"I'm talking about luck or unexpected things that happen, lack of run support. It's amazing. When we do get him some runs, he might strike out 12 batters and then have one bad inning."
Lee -- who won his first game this season at Citizens Bank Park on Sunday -- is 3-7 with a 3.67 ERA. He was on the DL with a left oblique strain from April 21-May 9.
"I get mad, I get upset and frustrated," said Manuel. "I'm a Vince Lombardi guy -- I don't like second place, losing. I'm a first-place guy. For us not to be able to get things together has been difficult, hard for me to accept.
"I look back [and ahead], and there's things we've gotta do. The biggest thing we have to do is play baseball better. From the whole standpoint of the game, we have to hit better, we have to field better, pitch better. It seemed like everything snowballed on us, but the biggest thing is we haven't played sound baseball."
Manuel said he's determined to get his message across to the underachievers.
"There have been times when I got things off my chest," said Manuel, who's had some memorable vintage Manuel clubhouse meetings/lectures. "There are things I do I don't want people to know about. When I say something in our clubhouse, it won't be public."
It's difficult to picture "Good Ole Charlie" out of a baseball uniform, but after his contract ends with the Phils next season, he's not sure what his future holds. Manuel has always wanted to go fishing in Alaska, loves to play golf, tinker with cars, collect coins and relax at his home in Winter Haven, Fla.
Forget all that. My guess is he's a baseball lifer.
"I'm not going to say I'll walk away after next year," Manuel said. "I'm very satisfied where I'm at. I do know this: I want to get back to the World Series. The rest will take care of itself.
"But I'm also open to anything the Phillies want to do. I don't think I'm ready to retire, but at the end of next year, I'd like to sit down with [team president] David Montgomery and [general manager] Ruben Amaro Jr. and get a feel for what they're thinking."
As Manuel got up to leave, he looked back and, without prompting, almost shouted: "No matter how you say it, we just haven't played good enough baseball to have a winning record."
Enough said. He didn't look back again.
Hal Bodley is the senior correspondent for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.