Colin Kaepernick came two yards short of delivering the 49ers their second win of the season. Before that loss, Trent Baalke said he took reponsibility for the Niners’ lost season. (Charles Trainor Jr./Miami Herald/TNS)

Kap shakes off questions about future as Baalke plans for it

The 49ers’ season was functionally over weeks ago, leading many to look to the team’s future.

One of the major questions confronting every bad team is how they’ll address the most important position in the NFL: quarterback. For the Niners, that means they’ll have to decide between holding onto current starter Colin Kaepernick or letting him walk in the offseason, as his restructured contract allows.

Kaepernick has continued to improve since taking over the starting role in Week 6 against the Buffalo Bills. Last Sunday, he threw for 296 yards and rushed for another 113 with three touchdowns against the Miami Dolphins. His constantly improving play has led many to wonder if the 49ers will keep him as they develop their quarterback of the future — presumably, someone they draft with their eventual high draft pick.

Keeping Kap might also lead to more wins as quarterbacks who have a rapport with their head coaches generally succeed at higher levels.

“I feel like I’m getting more and more comfortable in this offense,” Kaepernick told reporters on Tuesday as the team gets ready for the Chicago Bears in Orlando. “Ultimately, I think that’s what it comes down to for a quarterback is getting comfortable in an offense, really getting your feet settled in, getting that foundation to be able to go out and just play freely and this offense has been great for me in that way.”

But when asked if he’s looking to establish a connection with head coach Chip Kelly like some of the other great teams of the last decade (the New Orleans Saints’ Sean Payton and Drew Brees, for example), Kaepernick demurred.

“I’m focused on Chicago this week,” Kaepernick said. “I’m not thinking that far down the road.”

One person who is clearly looking to the future, though, is embattled general manager Trent Baalke.

“I’ve been watching the college games a lot right now,” he said on KNBR before the Niners lost to the Dolphins. “The free agent market, getting that lined up. So we’re spending a lot of time doing that. We’ll have the scouts come in December. There’s a lot of prep work going into the next two, three months after the season ends.”

He said during the radio appearance that it’s getting harder to remain an optimist in light of the team’s play this season.

“I don’t know if you do keep yourself up, or positive,” he said. “I think you are drained. It’s a draining experience. I feel bad for the fans, I feel bad for a lot of people, the ownership in particular.”

He went on to say the York family has given him all of the resources he needs to succeed and that “it falls strictly on my shoulders.”

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