PHOENIX — First there were none. Now, there are two. But who, who will be the one?

New 49ers coach Kyle Shanahan needs a starting quarterback next season, and he needs someone to carry the torch for him as he and general manager John Lynch try to turn the franchise around.

San Francisco added free agents Brian Hoyer and Matt Barkley and have the No. 2 overall pick in next month’s NFL draft. Speaking Wednesday at the NFC coaches’ breakfast at the NFL owners’ meeting, Shanahan said he knew that his starting quarterback wasn’t going to be Colin Kaepernick.

Kaepernick opted out of his contract before the 49ers released him, after meeting with Shanahan and Lynch in February. The coach told him it wasn’t going to work out — “it’s not you, it’s me,” to borrow from the breakup handbook.

“Colin’s had a great career, and he’s done some really good things,” Shanahan said. “I think Colin has a certain skill set that you can put a specific offense to it that he can be very successful in.

“When we first looked at it … that wasn’t necessarily the direction I wanted to go. The type of offense I wanted to run was somewhat different and that’s why we went that type of direction.”

Kaepernick, who started 64 regular-season and postseason games for the 49ers, remains a free agent. NFL Commissioner Roger Goodell was asked Tuesday whether Kaepernick is being blackballed by owners over his on-field social protests last season. (Goodell said he hasn’t heard that to be true.)

Hoyer, an eight-year veteran with six teams, is a much better fit, Shanahan said.

“All these questions about what I like in a quarterback, Brian is like that,” said Shanahan, who was the offensive coordinator with the Browns in 2014 — Hoyer’s second season with the team. “He’s obsessed with the game. He will learn your offense. He’ll be able to execute and run it.”

That allows his teammates to do their jobs.

“If your quarterback can’t execute it and go through it, it doesn’t always matter what the O-line or the receivers are doing,” Shanahan said. “With Brian, you have a very smart guy who works at it, will hang in the pocket and is fearless, will keep his eyes down the field and deliver the ball to the right spots. It gives people a chance to be successful.”

If Shanahan and Lynch want a quarterback with the No. 2 pick in the draft, they’ll have their choice of anyone available because the Browns, who have the top pick, have all but ironed Texas A&M pass rusher Myles Garrett’s name onto a jersey.

“It feels good to be in a situation where we do have the second pick of the draft,” Shanahan said. “It’s one that I hope to not be in again, but it’s nice coming in and having a lot of options.”

So, so many options.

“We could trade and grab more people,” he said, “and if not, we’re going to get a good player with the second pick in the draft, and regardless of what position that is, we have to get the best player available.”

Is that player a quarterback? Probably not, but why would Shanahan tell you? Ready-to-play quarterback or not, Shanahan said the 49ers will still need to be patient.

“No one can guarantee anything,” Shanahan said. “Everyone is just looking for that franchise quarterback and people have found them with the first pick of the draft and people have found them in the sixth round.

“Just because he’s the first guy taken doesn’t mean he’s the going to be the best guy. Sometimes the last guy can be the best guy. You never know.”

Vic Tafur is a San Francisco Chronicle staff writer. Email: vtafur@sfchronicle.com Twitter: @VicTafur