I read it's 18 million/year because it's an extension and you have to count this year. With NFL salaries only going up and the salary cap going up, this deal won't look too bad as long as he makes even just modest progress. Every team will have more salary cap room and I imagine that other QB's will be getting over 20 million/year. If Kaepernick does reasonably well this upcoming season, you can bet that there would be a handful of teams offering him a huge contract.
And THAT is the kicker. You just locked him up early, before you had to, and have no idea if he can even make the next step. You could have made it through this year, and then tagged him if you had to and saved money. That's two years to find out what he's got between the ears.
It's great that he wrote himself a letter saying he would be a QB and he can throw a fastball, but can he find the second option before he tucks tail and runs. He won't have those legs in a couple of years, and then what's he gonna do? At least Vick/McNabb/McNair/Young could all actually play the QB position.