For me, the issue is the preservation of character and changes. The Dark Knight Trilogy is different from Batman the Animated series but they're internally self-consistent.
Well, sure, then I don't see the problem. A canon is internally self-consistent too, for the most part, and its tie-ins constitute side or spinoff continuities (if they have continuities rather than being strictly standalone). With Trek, for instance, we've got the '80s novel continuity (loose as it was), the DC comics continuity, the Malibu and Marvel comics continuities, the modern Pocket novelverse, and
ST Online, as well as the various standalones. Each is more or less internally consistent; they just differ from one another.
And like I said, not every story has to be about change and ongoing consequences. Standalones are just as valid. Indeed, ideally every story should be completely fulfilling in and of itself. If a story
depends on what happens in other, later stories to be of any worth, then that means it isn't really a complete story, just a fragment of one. Too many writers use serial storytelling as an excuse to be lazy and never tell a complete story, just using cliffhangers and twists as a substitute for satisfactory resolutions, raising question after question to obscure the fact that they have no answers in mind.
Superman Returns illustrates, to me, how canon can go terribly wrong too. If you're one of the three people who liked Superman 3 (such as myself) or Superman 4 (ditto), it's the director saying that he doesn't think your stories "count" which is mildly insulting but I'll get over it, I'm a big boy.
Again, it's only insulting if you make the mistake of seeing canon as a value judgment. Choosing to take your own story in a different direction from someone else's is not an insult, it's just a choice to exercise creative freedom. Look at the
Crucible trilogy. David R. George III chose to write a TOS trilogy that acknowledged only TOS and TAS themselves, not anything from the novel continuity. That wasn't a dismissal of the novelverse's worth, just a decision to tell a story that went in another direction.
Sure, in the case of
Superman, Singer made the decision to disregard those movies because he and others didn't like them. But there's no reason you should take that personally. Other people's likes and dislikes don't cast any aspersions on your own. If the story matters to you, if you found it satisfying, that's all that should matter.
Canon says "what is the official version of this story."
In a sense, but what I've been trying to get across for some time is that it's not some formal declaration on a certificate somewhere. Canon is just a word we use to refer to the work done by the primary creators. It's really more a term of literary/film criticism, of analysis and categorization done by outsiders evaluating the work. Yes,
sometimes the creators or their proxies choose to make statements about what should be regarded as part of the canon, as Roddenberry or Lucasfilm have done. But that's the exception, not the rule. And it's generally done more to clarify things for the audience than to create some categorization that would otherwise not have existed. Remember, the first people to use the word "canon" in reference to a fictional work were fans and critics of Sherlock Holmes. There were enough pastiches and fanfics of Holmes done by authors other than Doyle that it became necessary to distinguish between Doyle's own Holmes fiction, which they nicknamed the canon by analogy with church usage, and Holmes fiction by others.
What the core creators produce simply
is the canon. That's not something that has to be officially declared or designated, it's just the word we have come to use for that particular thing. And I've explained why it's difficult and generally impractical for the core creators to maintain perfect consistency with other creators' work when they're too busy with their own to directly supervise it. Canon vs. non-canon is not about passing judgment or establishing a hierarchy of worth, it's just about the practical realities of series creation. Separate creators' works are, by their nature, separate. And since different creators have different ways of interpreting a work, their approaches may not entirely mesh with the canonical approach. That's not wrong, since exploring variations on a theme is a basic part of creativity. But it does mean that different versions might not be compatible, that it might not be feasible to treat them all as a uniform continuity. Again, not a rejection, just a difference.