I've been thinking about accusations of "cliché" scenarios--final battle, Petunia has a deep secret, Neville's memory is wonky because someone did a charm on him after he saw his parents tortured, other things like that, things that lots of people have done, to a point where they read as clichés, but which I would argue don't deserve to be treated that way.
When addressing a negative fanon cliché, it tends to be something that's bounced around fandom, has no particular basis in canon, and isn't related to issues raised by the books. In the case of the kinds of scenarios above, the second two problems are entirely moot and the first may or may not have any influence on it.
Yes, it's true that "Petunia has a dark secret" is a hook that's been used in a lot of existing fanfics, but someone who uses it in a story hasn't necessarily picked it up from other fanfics. It might have been, it might not have been; the handling of it is the real test. It's a scenario that can easily be arrived at independently.
In other words, it has a basis in canon and is related to issues raised by the books. The same is true of the "final battle scenario" and Neville's memory and any number of other things that fic writers are prone to writing. A lot of them strike me as things that are actually likely to happen in canon... should a fic writer be penalized for guessing canon right? Should JKR be penalized when she writes it because people figured out a scenario that made sense in terms of what she'd already written?
Any time you're working with the canon storyline (as opposed to a romance subplot or an AU or whatever), you're going to be speculating on things based on what's there in the existing text. Starting fresh, there are things that would tend to come to the surface. Harry's gathering a group of allies; Voldemort is regathering his allies (and possibly recruiting new ones). It's a sensible guess that these groups will come into conflict with one another at the climax of the story. It's not necessary that it's so, but it's a highly sensible guess, and therefore it appears in a lot of fics if they happen to deal with the end of the war. Petunia has some curious behaviors, gets odd letters from Dumbledore saying "Remember my last," and is the sister of Harry's mother... nothing absolutely says that there's more to her than meets the eye, but it's sure not an odd guess. And so on, and so on.
Scenarios that can be arrived at by rational extrapolation of existing canon--things that could and might actually happen in books six and seven--are fair game and logical guesses, not clichés, at least not in the sense of being the lazy writer's easy grab off the plot shelf.