INDIANAPOLIS — “Nothing’s changed,” Scot McCloughan was saying Thursday, even though plenty had changed since the end of the 2007 season.

Since then, McCloughan, the 49ers’ vice president of player personnel from 2005-07, was promoted to be the club’s general manager. Also, owner John York stripped head coach Mike Nolan of the final vote on personnel decisions and gave that to McCloughan, too.

But for McCloughan and Nolan, this Combine may as well be last February’s Combine as far as their roles go. McCloughan is the personnel guy, but Nolan is still the face of the 49ers — and still has an opinion on personnel. That’s the status quo McCloughan was talking about.

But should McCloughan and Nolan fail to find common ground when it comes to evaluating a free agent or making the call on a draft pick … well, that’s when things will change for the Niners.

“The final say right now, if it comes down to that, if there’s a disagreement, Scot would have the final say,” Nolan explained.

Nolan lost that power after his team lurched from preseason darling to an offensively inept 5-11 club saved only from total embarrassment by a proud defense and third-string QB Shaun Hill, buried behind 2005 No. 1 overall pick Alex Smith and Trent Dilfer on the depth chart until injuries to both Smith and Dilfer gave him a chance to play.

Along the way, Nolan got into a nasty dispute with Smith about the quarterback’s injured right shoulder. Smith told the San Jose Mercury News that Nolan was trying to turn his teammates against him by questioning his toughness. Smith had shoulder surgery, Nolan lost face, and the relationship between both men will be scrutinized until one or the other leaves.

Who would make such decisions for the Niners — and whether anyone would be motivated to make such decisions — is unclear. York surprised some observers by bringing Nolan back for 2008, and he signed off on the contract given to Smith in ’05 that could be worth as much as $49.5 million. Smith is only 23 years old; he’s too young to give up on but just old enough to cross your fingers and hope rapid improvement is around the corner. (He’s also old enough to be in a fight for his starting job with Hill this offseason.)

McCloughan certainly has more pull than he had before, but you don’t get the sense he’s eager to use it. And Nolan still has a voice — and believes the team’s decision makers need to be moving in near-lockstep.

“The important thing about running the top of your organization correctly,” Nolan said Thursday, “is there aren’t a lot of those (differences when it comes to making personnel decisions), and to this point there have not been, and I do not foresee any going down the road.”

The Niners’ draft record in the Nolan-McCloughan era has been mixed. Say this much: They have made enough prudent first-day picks to build a talented core of young players. Selecting RB Frank Gore in Round Three of the ’05 draft was a masterstroke, as was taking ILB Patrick Willis last year. Rookie OT Joe Staley has Pro Bowl potential. OLB Manny Lawson, should he recover from a knee injury suffered last season, can be special, as can fellow ’06 first-round pick Vernon Davis, an athletic tight end.

But whether Smith will ever be anything more than an average quarterback is anyone’s guess. What’s more, the team hasn’t used its second-day draft picks to replenish its depth as well as it has needed to do. The Niners lack a top-flight wide receiver and must bolster their secondary and pass rush.

The Niners’ ability to evaluate their own talent has to be questioned, too, given how well Hill played down the stretch — and only after the ineffective Dilfer suffered a concussion in the 13th game of the season. Hill, the former No. 3 quarterback, completed 68.4 percent of his passes with five TD passes and only one interception in three appearances. That’s too small of a sample size to get overly excited about, but Hill’s command of an offense that was without direction for much of the season makes you wonder what he could have done with more playing time. The 49ers signed him to a three-year deal before the upcoming free-agent period, and he looks to have a legitimate shot to push Smith.

Nolan didn’t talk much about Smith on Thursday, although he did praise the young quarterback’s intelligence and said he didn’t anticipate Smith taking too long to get accustomed to new offensive coordinator Mike Martz’s attack, considering the terminology and scheme will largely be what it has been for the past three seasons.

“Although Mike’s got a lot of ideas and is very creative, it’s all within the framework of what we already do,” Nolan said.

What the Niners have done in three years under Nolan is ride a roller coaster of expectations: They started low in ’05, crept upward in ’06 and rose to new heights before the ’07 season, when San Francisco was seemingly everyone’s postseason sleeper. Then came the plunge of ’07.

No one would be surprised if the ride is soon over for Nolan. McCloughan, new promotion on the résumé, probably has more job security.

The easiest way to garner more of that, of course, is to strike when the preview magazines are predicting doom and your division rivals see you as two “must-win” line items on the schedule. Remember: Everyone rushed to overlook the Niners’ flaws last offseason — and this was before we knew how good Willis would be and what Staley would mean to that offensive line.

So understand the optimism of the Niners’ brain trust. “I think we’ve got enough good people around us in the personnel department and on the coaching side that we’re going to try to get it right,” McCloughan said.

And understand if the whole situation in San Francisco looks like a dress rehearsal, with the major players still tweaking their roles, still feeling out where they need to be in every scene. Nolan still has the most lines, but McCloughan will get the final sentence of dialogue, more than he ever did before. York? He waits in the wings.

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