Here are five reasons why:
<b>1. Accuracy.</b> Wilson has improved in this area and Kaepernick has regressed. This season, Kaepernick is completing 57.8 percent of his passes — stink-o-rama. Wilson is completing 64.9 percent of his passes — great-o-rama. When Montana was Wilson's age, Montana completed 63.7 percent of his passes. Try to get your head around that one.
<b>2. Elusiveness.</b> This really isn't Kaepernick's strength. He's fast when he gets his long stride turning, but he's not elusive in the open field or in the pocket. Elusiveness always has been one of Wilson's best traits. He runs circles around defenders, like Young used to do, and he sure runs circles around Kaepernick.
<b>3. Improvisation.</b> Another trait Wilson shares with Young. When Young was scrambling, he always knew when to pass, when to run and when to pump fake. These things were like breathing for him, and they're like breathing for Wilson. This season, Kaepernick has not been a good improviser. He's been mechanical, like Alex Smith.
On Wednesday, Jim Harbaugh gushed to the Bay Area media about Wilson's ability to improvise: "(He has) that feel that only so many quarterbacks have had that have ever played the game — to extend plays."
"Does Kaepernick share that ability?" a reporter asked Harbaugh.
Harbaugh paused and said, "I think they're both very talented quarterbacks." He could have said, "Yes, Colin shares the ability to improvise." But he didn't. Harbaugh didn't give Kaepernick praise he doesn't deserve. Finally, Harbaugh added, "They both throw really well from the pocket, too."
<b>4. Passing from the pocket.</b> Even though Wilson is a peanut and Kaepernick is a giant, Wilson is a better pocket passer. On Monday Night when the Seahawks scored 27 points in the first half against the Saints, Wilson completed 10 of 13 passes from the pocket — 77 percent. Wilson sees the whole field and goes through more reads during his passing progressions than Kaepernick who tends to stare at his first read like someone lip-reading a menu and, if the first read isn't open, Kaepernick just runs.
<b>5. Composure and preparedness.</b> This is where Wilson has separated himself from Kaepernick the most. Wilson already carries himself like Peyton Manning. Wilson understands NFL defenses, understands situational football and understands how to act like the face of a franchise. Kaepernick forgets how many timeouts he has and runs out of bounds when he has to stay in bounds — boneheaded stuff. Kaepernick rejects being the face of the franchise. Look at any of his press conferences.
And ever since Kaepernick's last three plays of the Super Bowl when he failed at the goal line, he has failed under pressure. This season, he has lost to every team he's faced likely to be in the playoffs, and in fourth quarters his QB rating is 51. When he's behind, his QB rating is 58. Compare that to Wilson, whose fourth-quarter QB rating is 93 and whose QB rating while losing is 94. Like Montana, Wilson is cool under pressure. But Kaepernick is unsure of himself when things don't go his way or things get tight.
I'm throwing in a bonus reason why Wilson is better than Kaepernick, and it has nothing to do with either quarterback.
<b>BONUS REASON:</b> Scheme, the thing the 49ers hate talking about.