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Even before Kaepernick took the field against the St. Louis Rams last week, many 49ers fans believed he was "the future" and Smith was "the present."
If that was the case this offseason, then why did the 49ers sign Smith to a three-year deal. instead of, say, a one-year deal?
Maybe that was simply what Smith was demanding. Maybe the 49ers didn't want to risk only having Kaepernick in case something went wrong in his development. Maybe it was a bit of both. Regardless, by completing that deal, the 49ers knew that they'd have both Smith and Kaepernick under contract through the 2014 season.
Smith is only 28. He could conceivably play at a high level for another 10 seasons. You could argue that he is just entering his prime. He took the 49ers to the NFC title game last season. He won 13 regular-season games. He had a respectable 90.7 passer rating.
I think San Francisco gave Smith that contract believing that he'd be the starter for most of it, if not all of it. Maybe Harbaugh was hopeful that Kaepernick, who admittedly has better physical tools, would take the reins, but there was no guarantee that he'd ever realize his full potential.
Plus, it makes no sense to have an $8 million backup.
With both players signed for the same amount of time, Harbaugh was basically letting the two signal-callers audition for a contract extension for three years, knowing that if Kaepernick put it all together at any point that he could trade (or cut) Smith.
Before the Bears game, I don't believe Harbaugh was sure that Kaepernick was his starter of the future. Smith was getting the job done, and had Kaepernick not dominated like he did, he may have been the backup to Smith for the rest of his contract.
Instead, Kaepernick dominated, leaving most convinced that he must be the starter of the future in San Francisco.