Well I do agree with the first part of your post...
Their first years were pretty close, Harden had a better PER (14-13) for whatever that is worth, which admittedly isn't much. By win shares, Harden was much better, which once again, may not be worth much. But I don't really think you can definitively say that Flynn was better than Harden as a rookie. Flynn struggled to score efficiently (which was always going to be an issue for him) and Harden had a 55% true shooting, which for a rookie is really good.
Flynn's career was derailed by injuries, to be sure. But his rookie year, to me, was nothing more than ok. He's a short guard who was always going to have trouble scoring with good efficiency, and his rookie year did nothing to dispel that knock on him. Seems like more often than not, a player who sees his draft stock shoot up with a post season run is going to end up overrated. (I'm totally making this up but it makes sense).
I guess the bottom line is because of the injury, everyone in this case is going to think they were right.