It's ironic you bring up taking care of the football as many people post that pick of his 4 Int game (99% probably having no idea that represents over 13% of his career Int). I would note that his passing and TD's per game stats are affected by the fact he averaged must less attempts per game than more prolific QB's. His TD% and yards per attempt are very in line with someone like Matt Stafford, just one guy averaged 25 attempts a game, while Stafford averages 38 a game (38 is actually pretty crazy high, Rodgers is like a 33 while Brady/Manning were around 35). I agree some of his flaws were covered up, but I'd also point out many of the people who shit on him pile on so much that wasn't just on him, as well (stuff like his record his last year, despite being on an utter trash roster with no receivers and the dead last D in the entire league). Even the year he went to the Super Bowl, as good as that defense was for most of the year, they weren't holding their opponents to 14 or less every game or something.
Dude was never as good as some made him out to be, and I have serious doubts he's worth a shit to anyone after this much time away...but his last year and going into 2017 he was still fringe starter/good backup quality QB.
I watched him extensively in college and the pros because I had a friend who loved him. I agree with a lot of this. From the opposite side of the coin, very little of their success was based on him after teams adjusted to his skills. He was a flash in the pan and could have never been a longterm answer for a NFL franchise. His limited skillset and lack of improvement weren't on coaches or a lack of talent any more than his success was based off a massive amount of coaching and player talent during his extremely short stint as a good QB. The defense and running game were their bread and butter during those years.
While Alex Smith will never wow with his pure abilities, he also learned to manage his TOs as well under Harbaugh and provide a similar standard of success. Kaepernick was never a QB you could depend on to win you games consistently. His output ensured that, as you stated. For most Kaepernick defenders, they state bias as the reason he lost to Gabbert, when in reality it's because he couldn't fully grasp the offense and didn't have assloads of offensive talent to hide his weaknesses.
He's no worse than guys like Trubisky, Matt Moore, or Tannehill with the proper weapons and gameplan to maximize opportunities. He's just not even close to as good as his defenders keep preaching.