Former 49ers QB Steve Young is uncertain about new head coach Chip Kelly’s ability to work within the established system of Trent Baalke and Jed York. (Gene J. Puskar/AP)

Young among those questioning Kelly hire

What goes around comes round, as they say, but as it concerned the next 49ers head coach, few could have known that it would happen this soon.

One year after the Niners cut ties with Jim Harbaugh and his egomaniacal ways, they hired Harbaugh clone Chip Kelly to fill the position Thursday, a decision as risky as it was controversial.

Kelly replaced Jim Tomsula, a so-called players’ coach who was fired after a 5-11 season, his first on a four-year contract. Because of schedule conflicts, the former Oregon and Philadelphia Eagles coach will not be introduced locally until next week.

“Chip has a proven track record at both the college and NFL levels that speaks for itself,” CEO Jed York said in a statement. “We believe strongly that he is the right man to get this team back to competing for championships. I look forward to watching [general manager] Trent [Baalke] and Chip work closely to build a team that will make us all proud.”

At 52, Kelly was the recognized name and creative offensive mind the Niners had wanted at the position. Known for their hyperaggressive, up-tempo style, his Eagles teams consistently ran more than 80 plays per game, which put a premium on athleticism and physical conditioning.

“I would like to thank Jed, Trent, and the York family for this tremendous opportunity to be the head coach of the San Francisco 49ers,” Kelly said. “As one of the most historic franchises in the National Football League, I realize the high standards and expectations that this position demands and I embrace the challenges ahead. My immediate focus is to build the best coaching staff possible, one that will maximize the abilities of each of our players and put us in the best position to win football games.”

This season, the Eagles executed a play every 22.7 seconds, the fastest pace in the league. It ranked only 24th in yards per play, however. Such a frenetic tempo often exacts a toll on Kelly’s defenses, which historically lose effectiveness as the season progresses.

“Guess I might have to start running right now to get in shape,” 49ers wide receiver Torrey Smith tweeted shortly after the announcement.

Even though the list of qualified candidates was short, Kelly was not in demand after a tumultuous 2015 season, one that finished with questions about his leadership, communication and talent evaluation skills. Among the biggest disappointments in the league, the Eagles had a 6-9 record when he was released with one game left to play. He left with marks of 26-21 in the regular season and 0-1 in the playoffs.

Along the way, doubts flared about how effectively Kelly could work with players and management. Like Harbaugh, Kelly has a reputation as a control freak who demands input in personnel decisions, which he had for much of his Eagles tenure. That represents an obvious conflict with Baalke, who has wielded that authority in recent years. Baalke reportedly will continue to have the final say on such matters.

“The fact that [Kelly is] in San Francisco, [that’s] great, but now what are we going to do?” asked Steve Young, ESPN analyst and Niners legend. “The most I worry about [is], Chip Kelly is a very strong personalty. Trent Baalke, general manager, gives nothing [in the way of control] to the coach. That was most of what was at the bottom of the problem he had with Jim Harbaugh — strong personality [working with another] strong personality. How does that work out?”

Yet given his shaky status after a last-place finish, it remains to be seen how much longer Baalke will remain the primary decision-maker. If the young talent base that Baalke assembled were to disappoint again next season, personnel chief Tom Gamble would be in line to replace him as general manager, an arrangement that he and Kelly no doubt would welcome given their close relationship in Philadelphia.

Perhaps not coincidentally, no sooner was Kelly dismissed on Dec. 29 than the speculation began that Tomsula might not return next season. The opportunity intrigued Kelly, who experienced his greatest success as Oregon coach and prefers the West Coast lifestyle.

“Chip possesses all the qualities we were looking for in our next head coach,” Baalke said. “He has demonstrated the ability to be innovative everywhere he has coached and has had great success throughout his career. Chip’s passion for the game and vision for the future of this team clearly stood out to us during the search progress. He is an extremely driven individual that I look forward working with.”

Kelly had support from several members of the Niners front office, Gamble being chief among them. Kelly and Gamble spent two years together in Philadelphia before Gamble was dismissed after the 2014 season, a decision that did not sit well with Kelly although he didn’t stand in the way. Rather, he won a power struggle with Eagles executive Howie Roseman, but failed with the personnel control he was given by owner Jeffrey Lurie.

From 2010 to 2013, Gamble was Niners director of player personnel. In that capacity, he worked with Baalke on personnel matters at the college and pro levels. Quarterback Colin Kaepernick, fullback Bruce Miller, safety Eric Reid and linebackers NaVorro Bowman and Aldon Smith were among the players drafted in that time.

In his first two seasons, Kelly guided the Eagles to consecutive 10-6 records. Some hailed his unorthodox offensive schemes as the wave of the future.

Piece by piece, Kelly began to dismantle the core nucleus as he attempted to mold it in his image. Along the way, whispers grew audible that he either could not or would not relate to NFL-caliber athletes, African-Americans in particular.

After his position was terminated, one-time Eagles defensive assistant Tra Thomas went so far as to tell Fox Sports that players suspected a “hint of racism” in personnel decisions. In each of the last three seasons, Kelly approved the trade of a star black player — wide receiver DeSean Jackson, McCoy and wide receiver Jeremy Maclin.

“[Kelly is] uncomfortable around grown men of our culture,” ex-Eagles cornerback Brandon Boykin said after he was moved earlier this season. “He can’t relate and that makes him uncomfortable. He likes total control of everything, and he don’t like to be uncomfortable.

“Players excel when you let them naturally be who they are, and in my experience that hasn’t been important to him, but you guys have heard this before me.”

Kelly and his team were at the center of a race-related controversy in July, 2013, when a video of Riley Cooper surfaced after the white wide receiver was denied backstage access to a Kenny Chesney concert.

“I’m gonna come back and fight every n—-r here, bro,” Cooper threatened in reference to the black bouncers.

After conversations with team leaders, some of whom were black, Kelly allowed Cooper to remain with the team. Cooper was fined an undisclosed amount.

“I am so ashamed and disgusted with myself,” Cooper tweeted later. “I want to apologize. I have been offensive. I have apologized to my coach, Jeffrey Lurie, and Howie Roseman and to my teammates. I owe an apology to the fans and to this community. I am so ashamed, but there are no excuses. What I did was wrong and I will accept the consequences.”

Prior to the 2014 season, Cooper was rewarded with a five-year, $22.-5 million contract extension. Last season he caught 21 passes and two touchdowns.

“Coach Kelly bagged [Cooper] and he sent him off to have some coaching on how to handle race, I don’t know,” Thomas said. “But my question with that [is] when you look at who Riley Cooper is … if he was black and at a Trey Songz concert or something and he was talking to a white person or a homosexual like that, and he was gay-bashing, would he still be on the team?”

Several ex-Eagles players haven’t forgotten that Kelly did to “ruin” the team, as Jackson put it recently.

“I’m a firm believer that bad karma comes back on you,” Jackson said earlier this month. ”When you ruin a team like that, you do things to people’s families, you release people, you trade people, you get rid of good players who build something with the community, with the fans, with the kids — to have a guy come in and change up the team like that, I just believe in karma.

“I don’t have any bad words to say about him as far as what he feels he needs on his roster. But the guys that were on that roster created something special, from Jeremy Maclin to LeSean McCoy to Trent Cole to Todd Herremans and myself and Brandon Boykin. … It goes on and on and on. When we were there, we were a brotherhood. So for everyone to go their separate ways and to see how it all ended up, it’s a very sad thing.”

In four seasons, Kelly posted a 46-7 record at Oregon and turned the Ducks into a national power. He has had much success in the development of quarterbacks, namely Marcus Mariota, the 2014 Heisman Trophy winner who carried the Ducks to the national championship game after Kelly left.

Kelly’s next project may be the enigmatic Kaepernick, whose athletic skills fit his system. The arrival of Kelly may be the only reason that Kaepernick is still around on April 1, when his $11.9-million salary for next season becomes guaranteed.

Blaine Gabbert finished the season as the starter after Kaepernick was benched because of injuries and ineffectiveness. The organization also has the No. 7 pick in the draft, probably not high enough to select Cal product Jared Goff as its quarterback of the future.

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