SANTA CLARA, Calif. -- On paper, it looked like a match made in football heaven.

Of all the head-coaching jobs that came available last January, the Denver Broncos' opening was one of the most appealing. And on the list of coaching candidates, Atlanta Falcons offensive coordinator Kyle Shanahan sat at the top.

If that simple equation wasn't enough to form a match, there were the longstanding ties Shanahan has with the Broncos. The Shanahan name still rings out in Denver like Marlo Stanfield on a fictional Baltimore street corner. As the son of two-time Super Bowl-winning coach Mike Shanahan, Kyle Shanahan spent many of his formative years in Denver, watching his father coach the likes of quarterback John Elway to the game's highest peak.

Yet when the Broncos and San Francisco 49ers met for this week's joint practices, Vance Joseph stood on Denver's sideline while Shanahan was in charge of the Niners. Shanahan, it seems, was one of the few who seemed to know that he wasn't going to be the Broncos' next coach.

“I just had this gut feeling that I wouldn’t," Shanahan said. "I went into the interview, I really enjoyed it, meeting with those guys. I hadn’t seen them for a while. But yeah, I never felt like it. I felt after the interview I made it hard on them, but I always had a feeling that I wasn’t.”

For the son of a successful football coach, home is generally a relative term, most often found where the people you're closest to reside. In Shanahan's case, that's Denver. So when Shanahan, who was still coaching the Falcons in the playoffs as he went through the process, interviewed with Elway, many viewed his hiring as a fait accompli.

But when it came time for Elway, now the general manager and chief decision-maker in Denver, to choose the head coach to replace Gary Kubiak, it was Joseph, not Shanahan, taking the reins.

"I knew Kyle was going to get an opportunity, and if it wasn’t this year, it was going to be soon," Elway told ESPN on Thursday. "He’s just a guy that has tremendous knowledge of the X’s and O’s of the game and has shown that with the success he had in Atlanta and wherever he’s been offensively -- they’ve always done very, very well. And so his knowledge of the game is as good as there is in the league. It’s just a matter of finding the right fit. I’m very happy with Vance, but Kyle wasn’t too far behind just because he has that knowledge. There’s no doubt in my mind he’s going to have a lot of success in this league."

Returning to his second love

Although Elway came away impressed with the interview, Shanahan didn't see Denver as the place for him to land his first head-coaching job. Not that he wasn't interested; he certainly was. Reflecting on it this week, however, Shanahan revealed he envisioned something different for when he finally made the leap from coordinator to man in charge.

“Always deep down, I think, I’d rather [be in] a different situation," Shanahan said. "But I loved Denver. I loved growing up there. My family is from there. My wife’s family is from there. So it would be a hard thing to say no to when your family’s there and things like that. But by no means was that my situation of choice.”

What Shanahan was looking for was a job that could offer stability with a rich tradition and a blank canvas for him and a general manager with whom to mold the team in a shared vision. Coming off a 2-14 season, the 49ers offered all of those things, plus the patience to land Shanahan after Atlanta's run to the Super Bowl.

As an added bonus, Shanahan had a history with the Niners. His father was the 49ers' offensive coordinator from 1992-94. During that time, Shanahan tagged along with his dad to work, serving as a ball boy and doing whatever odd jobs he could to be around the team. If the Broncos were Shanahan's first love, the Niners were his second.

In coming back to the Bay Area, Shanahan saw an opportunity to restore one of the game's greatest winning traditions outside the shadow of his father's name and team.

"I drive in every morning, and on the wall I see ‘Faithful Then and Faithful Now,’ and I always think about that because that’s how I used to always feel back in the day," Shanahan said. "I grew up a fan of two teams. I was with the Broncos when I was real young, then it became the Niners going into middle school and high school. I was strong with them, too. That’s how I always felt being a Niner Faithful growing up, and now it’s kind of always weird when I drive in the morning and see ‘Faithful Then and Faithful Now,’ because it kind of hits me, and it’s like ‘Wow, I am back here.’ I kind of feel that a little bit each day."

In San Francisco, Kyle Shanahan saw an opportunity to restore one of the game's great franchises outside the shadow of his father, longtime Denver coach Mike Shanahan. Evan Pinkus/Getty Images

Dad's still a call away

In some ways, Shanahan's long history with the Broncos could be viewed as a reason the team wasn't a good fit for him. Following in his father's famous footsteps would have been a lot to ask for a first-time head coach, even nearly a decade after Mike Shanahan last coached the Broncos.

And while having family and friends nearby is a bonus, that could be viewed as a potential distraction. Those are all things Elway considered when looking at why Shanahan believed the Broncos might not have been his ideal fit.

"There’s no question," Elway said. "I haven’t been in that situation, but looking from the outside in, I can understand how that could be an issue. Plus you are coming back to where you were raised and friends and family and everything that’s back there, all of a sudden you might have been walking into a pressure-cooker, especially with the situation that we’re in, having won the Super Bowl a couple years ago, so the expectation level was very high. So I can understand what his thinking was on whether he wanted that job or not because [of] having grown up there and such."

Now that he's settling into his new job with the Niners, Shanahan is finding the balance between carving his own niche and leaning on his father for advice. Mike Shanahan spent time around the Niners during the spring but hasn't been present for any of the Niners' training-camp practices, though he has a standing invite.

Instead, father and son rely on technology to keep in touch. The Shanahans talked on the phone before the 49ers' first preseason game last week in Denver. They talked again the next day, with the elder Shanahan chiding his son for not calling a timeout after an explosive play near the end of the first half.

"He told me all the things I did wrong," Kyle Shanahan said. "I try to learn from him and argue with him a little bit on it. But I always talk to him about stuff to get feedback. He’s been a huge asset to me my whole life in that aspect.”

After a couple days of joint practices between Shanahan's two favorite teams, both the Niners and Broncos seem plenty happy about the decisions they made. The same can be said for Shanahan, who has forged a tight bond with general manager John Lynch in their first six months together on the job.

“I knew John interviewed him and was thoroughly impressed with him," Lynch said of Elway and Shanahan. "And I know that was a tough call. John’s very pleased with Vance. Obviously, quite a familiarity with the family, but [Elway] really came away, just like I did, impressed with Kyle. So it’s neat to see it work out for everyone.”