Their two biggest issues have been at arguably the two most important places: the head coach and quarterback.
They've lacked consistency and continuity in even the slightest regard as none of their experiments have worked out.
They're still evaluating who the best quarterback would be to give the starting nod, and here's five reasons why Harbaugh will end up going with Kaepernick.
While he may not be a refined quarterback from a mechanics standpoint yet, Colin Kaepernick has undeniable athleticism.
His elusiveness and ability to take off running with the football gives an added dimension to his game and allows him to evade pass rushers and make plays when there's nothing open downfield.
Jim Harbaugh has stated that one of his desired traits out of quarterbacks has been athleticism, and Kaepernick fits that mold.
As I said, a primary reason they've had recent struggles has been because of their incompetence at the quarterback position.
Alex Smith, J.T. O'Sullivan, Shaun Hill, Troy Smitth, Tim Rattay, Ken Dorsey: They've plugged in so many random players under center, and, frankly, all of them have failed miserably.
Perhaps that's why they went ahead and drafted Kaepernick with the hope that he'd break that trend.
With that being so, why would you even think about going back to Alex Smith?
Contrary to popular belief, young quarterbacks have had surprising success in the NFL as of late. Just take a look at what the likes of Matt Ryan, Sam Bradford, Matthew Stafford, Mark Sanchez, and Josh Freeman have been able to accomplish. All have had significant impacts on their respective teams and improved them far past the levels they were originally at when they were drafted.
That said, it plants a bright precedent for teams to follow. After all, it is a copycat league right?
The 49ers drafted Kaepernick and it's probably best for them to prepare him over the offseason and throw him out there to see what he's capable of doing. The fact of the matter is that you learn much more on the field than you do resting on the sidelines.
As I referenced earlier, the 49ers have been attrocious for a while now. In fact, they've posted only one winning season since 2002 and haven't been to the playoffs since then.
I'm sure the team definitely wants to get over that and move forward, and the best way to do so is by getting under a new regime and starting over.
While that doesn't necessarily mean binge dropping your entire roster, they've started the process by hiring a new head coach and drafting a rookie quarterback.
Sure, it's not guaranteed to be much better, but it'll help excite the fans and have them forget the past.
Jim Harbaugh is an offensive guru and a quarterback specialist. Just look at what he did with Andrew Luck at Stanford.
If he chose Colin Kaepernick out of the bunch, then it's clear that he likes what he sees and that the former Nevada star is his guy.
Harbaugh will probably be most effective if he feels comfortable with who's under center, and that is why I think he'll ultimately give the reins to Kaepernick.