When the going was good, nobody complained. When the going was bad, all of a sudden Colin Kaepernick’s defaults not only came out, they were magnified.

From 2012 to 2013, Kap was among the top QBs in the league, leading the 49ers to the NFC Title game two straight seasons and coming within one play of putting up San Francisco in the Super Bowl with less than two minutes to play.

That was good Kaepernick.

Bad Kaepernick showed up in 2014, and has seemingly gotten worse since then. The most common term being thrown around is that he looks like a deer caught in the headlights. Former Dallas Cowboys coach and two-time Super Bowl champion Jimmie Johnson gave an excellent analysis of Kap’s play:

Truth is, Kap’s deficiencies have always been there, but when the 49ers were winning, they went unnoticed. Now that they are crashing badly, they are glorified.

Blame Kap for his faults, but you cannot just blame him alone. There is enough fault to go around the entire organization.

49ers owners Jed York and GM Trent Baalke threw Kap under the bus when they decided to get rid of Jim Harbaugh as their head coach, then not finding an offensive minded coordinator to take over the departing Greg Roman.

Add the fact that the 49ers never fully addressed the flawed and limited wide receiver position, a seemingly old Vernon Davis who is a shell of himself, and a brand new right side of the offensive line, and you’ve got the makings of the lowest scoring team in the NFL, with Kaepernick taking a ton of flak for it.

Kap has always been below average on short passes- with his bread and butter being timed intermediate passes. He’s money on those. Anything other than that, and Kap is a heavily flawed QB, but with Roman and Harbaugh, and a top notch running game, his faults weren’t as noticeable. Now however, there is already a growing consenus that Kaepernick will be out of the Bay Area by next season.

I don’t know about that, but what I do know is that what is going on in San Francisco is messed up. How in the world did a franchise that finally dug itself out of the pits, go right back there two years later?

And how did a QB, who was an absolute badass a couple of years ago (i.e., going into Lambeau sleeveless and leading the 49ers to a win) go from that, to what the headline were just minutes after Sunday’s loss?

Mind boggling.

The regression of Kaepernick isn’t all his own, but it sure seems like it. Kap has a chance to make huge strides Sunday night when they take on the NY Giants in primetime, a game which could become another barn burner for the 49ers offense, or an awakening for a team looking for a spark, and a QB looking for something to cheer about.