The better news for the Phillies in this season of so much bad is that a scout from outside the organization agrees and was even stronger in his praise than Jordan.
"For all the grief the Phillies have caught in the recent past about getting older and not having any prospects in the upper levels, I now think they have some legitimate prospects in double A and triple A," said the scout, who did not want to be identified. "It looks to me like they have a real transition going on."
The scout added that the upper tiers of the Phillies' farm system compare favorably to the other teams in the National League East.
"It is better off than all of them with maybe the exception of the Nationals," the scout said. "They have more than the Mets, Marlins, and Braves in terms of prospects at the upper levels. Some of those acquisitions they made [at the trade deadline] really elevated their system."
With regular-season games wrapping up in the minor leagues this holiday weekend, here is a top-to-bottom review of the Phillies' minor-league teams.
Lehigh Valley (Triple A)
Best story. Kevin Frandsen and Erik Kratz started the season as career minor-leaguers with limited major-league playing experience. They are ending the season as staples in the Phillies' lineup. That was not the Phillies' plan, but both players have made the most of their opportunities and have a real chance to be part of the opening-day roster next season.
Best pitcher. This one is easy. Tyler Cloyd, a combined 15-1 with a 2.26 ERA at Lehigh Valley and double-A Reading, wasn't just the best pitcher for the IronPigs, he was also voted the best pitcher in the International League and won the Paul Owens Award as the Phillies' best minor-league pitcher. Now, he's getting his first look in the big leagues.
Best player. Domonic Brown did not have the best season at Lehigh Valley, but he did enough to persuade the Phillies to bring him back to the big leagues, and this time it appears as if he is going to stick around for a while. It remains to be seen if he is the long-term answer at one of the corner outfield positions.
Biggest disappointment. Righthander Austin Hyatt was 2-7 with a 6.33 ERA in two stints with the IronPigs and finished the year at Reading.
Other story lines. A total of nine pitchers spent time with Lehigh Valley and the Phillies this season. The best two at the big-league level have been Jeremy Horst and Raul Valdes, but the most potential still belongs to Jake Diekman. All three of those bullpen arms are lefties.
Reading (Double A)
Best story. Darin Ruf's amazing display of power was the best story not only in Reading but in the entire organization this summer. At one point last season he was relegated to designated-hitter duty because of first baseman Jonathan Singleton's status as one of the organization's top prospects. Then Singleton was traded to Houston as part of the Hunter Pence deal and Ruf's stock started to rise.
Now, he owns the Reading single-season home run record that used to belong to Ryan Howard, and he is likely to get a look in left field with the Phillies in September.
"I think there is more inventory on the position side in this organization than I was led to believe," Jordan said. "That obviously is led by Darin Ruf."
Best pitcher. Jonathan Pettibone was the best pitcher in the R-Phils' rotation this season and earned a late-season promotion to Lehigh Valley, where he has dominated.
"If Cloyd doesn't do what he did this year, he is probably the Owens Award winner," Jordan said of Pettibone.
Best player. Ruf has had the best season, but second baseman Cesar Hernandez showed all season why he projects as a future everyday second baseman in the big leagues. He also earned a late-season promotion to Lehigh Valley.
"He's Freddy Galvis with a better bat," the scout said.
Biggest disappointments. Trevor May will end the season with an elevated ERA, but Jordan was confident that he was headed in the right direction by the end of the season. Brody Colvin was promoted from Clearwater to the R-Phils in late July and continued to have severe command problems.
Other story lines. Tyson Gillies was suspended for berating a bus driver and missed significant time because of a concussion, but he electrified observers when he was on the field.
"I would pay to watch this guy play center field," Jordan said. "We have to find a way to develop him into an everyday major-league player."
Another exciting late-season story at Reading was the arrival of catcher Tommy Joseph and pitchers Ethan Martin and Kyle Simon, all of whom are considered big-league prospects.
"I expect Joseph to fly right by [Sebastian] Valle as their best catching prospect," the scout said. "He's a legitimate power-hitting catcher."
Joseph came to the Phillies in the Pence trade, Martin was part of the Shane Victorino deal with the Dodgers, and Simon was acquired from Baltimore for Jim Thome.
Clearwater (High A)
Best story. Jesse Biddle was the Phillies' first-round draft choice in 2010 and has had the added pressure of being a Philadelphia native trying to live up to the hype.
Consider this season another minor-league rung climbed with remarkable aplomb by the 20-year-old lefthander.
"I don't think we could have drawn up the year to have gone any better for Jesse," Jordan said. "He has got all his starts and innings, and he is better today than when started. He's a great worker and has every intangible you could want. Next year he'll be in Reading and hopefully it just continues."
Best pitcher. This distinction could have gone to any one of the three lefthanded starters in the Clearwater rotation. Biddle was joined by Austin Wright (eighth-round pick 2011) and Adam Morgan (third-round pick 2011), and they went into the weekend third (Biddle), fourth (Morgan), and fifth (Wright) in Florida State League ERA, and one (Biddle), two (Morgan), and three (Wright) in strikeouts.
Morgan was promoted to Reading in early August and continued to succeed. Wright was voted FSL pitcher of the year. We're calling this category a three-way tie.
Best player. Third baseman Cody Asche probably would have won a Florida State League batting title if he had not been promoted to Reading in late June. He was hitting .349 when he left the Threshers. After a slow start at Reading, he had a blistering August and could be the team's future third baseman.
"I like this kid," the scout said. "He's got a little Chase Utley in him and a little bit of Darin Erstad. I'm not sure he'll be an everyday player in the big leagues, but I definitely think he's a big-leaguer."
Biggest disappointment. Outfielder Anthony Hewitt has shown improvement over the last two seasons, but not nearly enough to live up to his status as the team's first-round pick in 2008.
Other story lines. Jordan considers catcher Cameron Rupp to be one of the most improved players in the organization. Tyler Knigge posted a 0.60 ERA before being promoted to Reading in late July. Reliever Lisalverto Bonilla was dominant at Clearwater and Reading before suffering a season-ending thumb injury before he was schedule to pitch in the Futures Game in Kansas City.
Lakewood (Low A)
Best story. Outfielder Kelly Dugan, the Phillies' first overall pick in 2009, had trouble staying on the field in his first two full professional seasons and experienced some hamstring issues early in 2012. Eventually, he got healthy and excelled.
"He has had a hell of a year," Jordan said. "He has hit for average and power, and the big key is he has been healthy. He is a much better athlete than I thought he was in spring training. I had a bad read on him in our camp and I told him that."
Best pitcher. Righthander Ken Giles, a seventh-round pick in 2011, went 3-3 with a 3.61 ERA in 29 games, including six starts, at Lakewood and finished the year at Clearwater. He projects as a future late-inning reliever, according to Jordan.
"He has the best arm in our system," Jordan said. "There is not one pitcher in our system who has made any more progress He has a special arm."
Best player. Third baseman Maikel Franco figured to struggle playing at the age of 19 in the South Atlantic League, and he did through the first half of the season. Since the end of June, however, he has played remarkably well, solidifying his status as one of the organization's best prospects.
Biggest disappointments. Outfielders Kyrell Hudson and Aaron Altherr have proven to be outstanding defensive players who are short on the offensive side.
Other story lines. Christopher Duffy has been the BlueClaws' best hitter, but he is 24 and cannot play anywhere other than first base. Hoby Milner, a seventh-round pick in June, excelled after joining the Lakewood rotation. Lefty Ethan Stewart has a big arm but needs to work on his command.
Williamsport (Rookie ball)
Best story. Switch-hitting shortstop Roman Quinn, the team's second-round pick in 2011, had team officials salivating over his talent during extended spring training, and he showed the world why at Williamsport with his speed and plate discipline.
"His speed is game-changing," Jordan said. "I think he set the team record for triples. He made some errors and most of them were throwing, but the progress he made defensively was really exciting. He has a chance to be as good a switch-hitting leadoff hitter as you will see."
Best pitcher. Geoff Broussard, the 23d-round pick out of Cal-Poly Pomona, excelled as the Crosscutters' closer.
Best player. Quinn was the Crosscutters' best player.
Biggest disappointment. Infielder Tyler Greene started at Lakewood and finished at Williamsport. He struggled in both places.
Other story lines. Third baseman Mitch Walding and leftfielder Larry Greene also made their professional debuts. Neither was spectacular, but both remain among the Phils' top prospects.
Gulf Coast League (Rookie ball)
Best story. Andrew Pullin, a fifth-round pick in June, batted .321 with a team-high .403 on-base percentage.
Best pitcher. Keive Rojas, a 19-year-old Venezuelan, went 4-1 with a 1.67 ERA in 17 relief appearances and struck out 42 batters in 321/3 innings.
Best player. Outfielder Carlos Tocci hit .278 playing most of the season at the age of 16. He turned 17 on Aug. 23.
Other story lines: William Carmona, the team's 11th-round pick in June, hit a team-high .348 with a .925 OPS and second-round pick Dylan Cozens had a team-high five home runs and 18 extra-base hits.
Contact Bob Brookover at email@example.com or on Twitter @brookob.