It seemed like such an easy decision three months ago.
Kaepernick, 26, was coming off a trip to the Super Bowl with the San Francisco 49ers in which he finished the 2012 season with the league's sixth-best quarterback rating. He was being compared to the top players at his position in the NFL.
Newton, 24, was coming off a 7-9 season with the Carolina Panthers in which he was ranked No. 16 in QB rating. His leadership and ability to win games when they meant something came into question.
But if you asked that same question today, as the Panthers (5-3) prepare to face the 49ers (6-2) at Candlestick Park, it wouldn't be such a slam dunk.
Newton ranks eighth in the NFL with a passer rating of 93.1. Kaepernick ranks 16th at 87.6. Newton has a completion percentage of 64.4, compared to 57.1 for Kaepernick.
Newton ranks No. 1 in third-down passing with a rating of 120.4. Kaepernick is fourth at 101.2. Newton is averaging 225.1 yards passing and 31.4 yards rushing. Kaepernick is averaging 198.0 and 36.8.
About the only statistic Kaepernick ranks ahead of Newton is in quarterback ranking since Week 6 -- and only barely. Kaepernick is first at 94.1 and Newton is second at 83.5.
Over their last 12 games, they both are 9-3 during the regular season. Kaepernick has the 49ers on a five-game winning streak. Newton has the Panthers on a four-game streak.
Kaepernick's biggest edge may be in talent around him. He has six former Pro Bowlers starting on offense. Newton has four in tackle Jordan Gross, center Ryan Kalil, wide receiver Steve Smith and running back DeAngelo Williams.
So Newton or Kaepernick?
In a lot of ways they're the same player. Both are in their third season. Newton is 6-foot-5 and 245 pounds. Kaepernick is 6-foot-4, 240. They even roomed with each other during the NFL combine in 2011 when Newton went No. 1 and Kaepernick No. 36.
"I don't want to compare myself to Kaepernick,'' Newton said. "He's an explosive player, don't get me wrong. But he does things that I can't do and I try to simulate some things that he does. I'm pretty sure our games are somewhat different in a lot of aspects.''
But they're alike in many.
“Yes, we have similarities,'' Kaepernick. "We’re both big, both fast, both can throw the ball well, have the opportunity to make plays for our offense.”
In the end, you probably can't go wrong with either.