FWIW, although Kaepernick sucked in the fourth quarter, all his turnovers occurred after the defense had already blown the lead. He had them ahead on the road going into the fourth quarter and the D couldn't hold it.
Also, Kaepernick is not nearly as bad a pocket passer as he's frequently made out to be. It's true that he can struggle with reads and progressions, but the "one-read QB" thing is way overblown. He was in the Top 10 this year in virtually every rate statistic (passer rating, QBR, DVOA, DYAR, Y/A, ANY/A, etc.). He had a low completion % but a high Y/C b/c the 49ers don't throw many short passes (it's mostly downfield stuff), and for a guy throwing mostly downfield he doesn't throw a lot of interceptions. And that's without considering his considerable rushing value.
I don't think Kaepernick could carry a mediocre team right now to a title right now, but those guys you named weren't carrying mediocre teams to contender status early in their careers either. Manning did have a great second year, but then regressed horribly in year 4, missing the playoffs when he was second in the league in interceptions. Brady didn't really become a guy who could carry a team until 2004, his fourth season as a starter (his ANY/A had a huge spike that season). Brees' first star season was his third year starting and fourth year in the league. Rodgers had a great second year as a starter but it was his fifth year in the league. Kaepernick has been a starter for only 1.5 seasons. If he doesn't show any improvement next year, that would be a worrying sign.
In 3 or 4 years, I could absolutely see Kaepernick being a top-5 QB. It would take some development and there's a reasonable chance he doesn't get there, but of the QBs under 27 (say, Luck, Newton, Wilson, RG3, Stafford, Tannehill, Dalton, Foles) I think Luck is the only one who's clearly a better prospect going forward.
As for the money, it's not just the absolute top guys who get $20m a year. Sure, I'd rather have Aaron Rodgers, but I'd also much rather pay Kaepernick $20m/year in 2018 than Cutler or Flacco or Eli Manning or an old Tony Romo.