The problem with pretty much all of your criticisms is they are purely subjective, and more have to do with what kind of story you prefer rather then any problem on the part of P4 in particular.

And change was forced upon the PC's of P4, they were dragged against thier will (A couple exceptions of course) when forced to accept different parts of themselves. The following step isn't forced upon them, but I kind of like that about it. While the realization was forced, it was soley their decision to act upon it. There was no obligation on thier part, just a desire to move forward.

And trust me, I didn't miss the point. There were a lot of points to it, and it doesn't change the fact they way they went about it was to make the PC's hold one of the biggest idiot balls I have ever seen. (SPOILER)A red herring doesn't work when the player knows it's blatantly not the case. All it does is serve to frustrate the player at the PC's blatent stupidity. And yes, it was in part to sell Naoto's intelligence. It showed her able to figure out something the PC's were completely unable too. Though regardless, all objectives were achievable without them being morons.