Let's look at the situation:
Why he's up for a deal: Kaepernick was a second-round pick in 2011. His contracts runs through 2014. He is set to be an unrestricted free agent in March, 2015.
What should he expect: It's an interesting situation. After Kaepernick led the 49ers to the Super Bowl in less than a full season as a starter, it would expected that Kaepernick would cash in as soon as he could -- after this season. It could still happen, but there is question of how much Kaepernick will get. Initially, it was expected Kaepernick would be a candidate to become the highest paid player in the NFL. Baltimore quarterback Joe Flacco signed a six-year, $120.6 million deal earlier this year to make him the highest paid player in the player.
However, Kaepernick, 26, hasn't had a dynamic second season. He hasn't been awful and he is clearly hurt by a lack of receiving options. But Kaepernick hasn't dominated games. If that continues this season, I'm not sure the 49ers -- who will have to clear money for a big contract, anyway -- would feel comfortable giving Kaepernick a Flacco-like deal. They may want to see Kaepernick have a solid 2014 first. The 49ers could offer a lesser contract, but I'd doubt Kaepernick would agree. So, it might be the logical decision for both sides for Kaepernick to go into his contract year without a deal. The 49ers could always franchise Kaepernick if a deal is not done by the 2015 offseason.
Prediction: A deal will get done. The 49ers love Kaepernick and his long-term potential. It's just that these colossal deals are tricky and everything has to be right for both sides, so it could mean it takes a little longer to complete than some expected. By the way, 2011 first-round pick Aldon Smith is also eligible to get a new deal after this season. But the team may wait because of his recent off-field issues. So, some big-money decisions by the 49ers could be delayed.