I don't think you understand them as much you think you do. First off unless you're looking at the All-22, or at the actual games, you can't tell if he's checking down because he's missing receivers or if there is really no one open. Once the receivers and tight ends run out of your tv screen, you don't know what was there unless there is a replay. And there is no replay on every play. You also don't know what the play called for. I read a blog that goes over his All-22 after every game, he's mostly checking down when WRs aren't open. He's rarely missing open WRs. Other times he is checking down to avoid a pass rusher. And this was the case last season, but Kirk would frequently get fooled by pre-snap disguised coverages and he needed to slow down his reads. He didn't do that last season and the turnovers mounted. This season he started out that way and then he began improving. His biggest weakness right now isn't turning the ball over, it's going off-script when a play is broken.
Yes, he occasionally will throw a bad pass. Eli threw a ton of bad passes yesterday and not only is he a starter, he is a two-time superbowl champion. Against New England, I watched Brady throw an awful pass directly to Perry Riley. All QBs throw bad passes, it's just the better ones learn from their mistakes and limit the amount of times it happens. Saying "he's been doing it through out his career" is debunked by the actual facts I provided.