All season long, the Phoenix Suns have been one of the feel-good stories in the NBA. Not only did they maintain their elite status after losing their best player, center Amare Stoudemire, to a knee injury in the preseason, but they managed to improve, utilizing a unique defensive system to complement their blazing offense.

Even though Detroit, San Antonio, and Dallas have posted better records, by mid-winter the Suns had become a favored dark horse. In January, they ranked in the top five in both Offensive and Defensive Efficiency (points per 100 possessions),and their average margin of victory suggested they were substantially better than their superb record indicated. With Stoudemire scheduled to return in March, the Suns figured to conquer the league.

Stoudemire returned last week, but suddenly the shine is off. The Suns got plastered in New Jersey by 38 points on Monday and followed that up with a miserable 22-point loss in Milwaukee. Meanwhile, Stoudemire’s return was short-lived. In his return to the court on Thursday against Portland, he enjoyed a stellar game, scoring 20 points and pulling down nine rebounds in just 19 minutes. But his production declined to six points and five rebounds in 17 minutes two days later against Denver.

By Monday night in New Jersey, the Phoenix big man was a complete nonfactor, going scoreless with two rebounds. He was slow, winded, and appeared to favor his surgically repaired left knee for much of the contest. It was no surprise when the Suns announced on Tuesday that Stoudemire would miss another few weeks and could be done for the season.

By the time Stoudemire returned to the Suns lineup, the paradigm had shifted. It wasn’t a question of ‘could the superstar take an elite team to a higher level,’ but ‘could he stop their fall.’ A relatively easy schedule and their ferocious offense had masked the fact that the Suns were starting to struggle defensively.

The Suns surprised nearly everyone when they led the league in Defensive Efficiency with a rating of 103.2 early in the season. But since January 1, they have played worse defense than even last year’s mediocre bunch, which finished 17th with a rating of 107. Currently, their rank has slipped to 10th at 105.7 and could slide further.

The Suns have a unique defense. Since no starter is taller than 6-foot-8, coach Mike D’Antoni devised a system in which the Suns pack the middle and force opponents to take jumpshots. Phoenix is among the league leaders in taking charges, fewest free throws allowed, and fewest assists – all as a result of keeping their opponents on the perimeter. “We want the game to come down to our jump shooter versus their jump shooters,” D’Antoni said earlier this season. “The more it does, the better our chances of winning.”

Of this week’s debacles, the New Jersey game has to worry the Phoenix braintrust the most. Yes, Milwaukee posted 132 points on the Suns, but it was a bit of a fluke. The Bucks made 18 of 32 shots (56.3%) from behind the arc, including 11 of 13 during a 46-point third quarter when they ran away with the game. Eleven of 13 is probably better than what Bucks sharpshooter Michael Redd hits during practice. For a team to shoot like that in a single stanza of a key game is a once-in-a-season occurrence.

The Bucks didn’t need to try to penetrate the Phoenix middle given the way their outside shots were dropping. The Nets didn’t have such a hot hand on Monday night; instead, they ripped through the Suns’ interior defense with guard Vince Carter and forwards Nenad Krstic and Richard Jefferson scoring at will inside. The Nets scored 36 points in the paint, and that was mostly accomplished in three quarters, after which point the starters yucked it up on the bench while reserves like Zoran Planinic and Lamond Murray practiced their jump shots during extended garbage time.

The Nets created several baskets by isolating Jason Kidd against his counterpart, reigning MVP Steve Nash. Kidd is substantially bigger than Nash, who is at best a middling defender. This forced the Suns to send double teams, and in response the Nets moved the ball quickly to the open man, often – Carter or Jefferson – on a drive. The Suns can expect to see more of this attack on Sunday when they play the Pistons. Detroit point guard Chauncey Billups often posts up his smaller counterparts. Other teams will undoubtedly pick up on this chink in the Suns armor and exploit it.

Some of the Suns’ problems may be solved with the return of ex-Knick Kurt Thomas in a couple of weeks. Thomas is due back early next month after missing time with a stress fracture in his foot. As Knicks fans know, Thomas is particularly adept at rotating quickly on defense to insure that neither double-teams nor pick-and-rolls result in mismatches. Thomas will also fortify the Suns defense with his uncanny ability to draw offensive fouls and guard taller players in the pivot.

Timing is the other factor in the Phoenix’s favor. At 47-23, the Suns own a six-game lead in the Pacific Division with 12 to go, so only a complete meltdown would cost them the division title. In addition, the Suns have an even larger lead – 7 1/2 games – over Denver, the leader in the Northwest Division in the race for the no. 2 seed in the conference.

The cushion will give the Suns time to get healthy for the playoffs, but their recent struggles indicate they may face a more competitive first-round series than anyone anticipated, and that they will almost certainly struggle in the second round. What looked like a great team and a sure bet for the Conference Finals may in fact merely be a very good one that is becomes an also ran in the rapidly approaching postseason.

mjohnson@nysun.com