Admittedly, I haven't watched a lot of his games, obviously nowhere near as much as you, but I've watched him closely 3 times: NC State this year, Carolina last year, and Pitt last year.
In the NC State game, I held a ODU ticket, so it ended up well, but I can't remember one time that he went significantly downfield. He completed something like 34 throws for 275 yards or so. It was all short. Same with Carolina last year, and they were behind the whole game. He had good numbers in the Pitt game last year, but didn;t throw the ball downfield much, as I remember.
Even against Eastern Michigan this year, he was 17-30 for 187 yards and no scores. In all the games I've watched him, he typically just throws very short, but efficiently. It wasn't a knock on him, although now that I read it, I see why someone would take it that way. I think he's really good, but his game typically isn't a downfield throwing game, based on what I've seen and the numbers in a lot of his games. In the game against Rice, however, he was chucking it like a mad bomber because Rice wasn't covering anyone downfield. Again, not a knock on Heinecke.