I would agree that people seriously overstate this films problems; it's nowhere near as great as 1 and 2, but it's still a good film overall, I'd say. While Spiderman 3's primary issue is a structural one, it's substance is still, for the most part, top notch.
Example: Harry finding out that his dad took his own life and sacrificing himself to save Peter; this makes no fucking sense. Harry should have found this out easily or his butler should have told him, (What the hell, man?) but I'd be lying if I said it wasn't genuinely tragic to see Harry and Peter as best friends for the first time since movie 1, only for Harry to be the person who ultimately pays the price for Peters mistakes. This story arc could have been fantastic if it was just cleaned up a little bit, and that describes the film as a whole; lots of good ideas getting in each others way.
I'll say this, if Spiderman 3 is endearingly flawed, The Amazing Spiderman is painfully average. It could be argued that there is less technically wrong with The Amazing Spiderman, but I cannot imagine anyone would compare it's heart or ambition to ANY of the original trilogy.
The Amazing Spiderman does nothing but go through the motions in an acceptable fashion, which would be less annoying if it wasn't so fucking unnecessary; there is nothing about it that the original trilogy didn't do at least mildly better, or at most MUCH better.
So yeah, I'll take Spiderman 3's messy, scatterbrained attempt at a story with real humanity over Amazing's clean, manufactured drivel any day.
Better yet, I'll just rewatch Spiderman 1 and 2; they're not that fucking old.