The only way to really avoid it at this point is for the big 2 to do the major reboot every couple of years just for that reason.
The problem is that reboots take a level of editorial fortitude that is rare in modern comics. And, doing them well takes a level of thought that is even more rare.
And, there is another problem...
Then there's the whole thing where writers just come up with a concept of "hey what if we did blank with character X?" and getting so stuck on how excited they are about what they just came up with that they don't even bother to think about whether or not it retcons or contradicts something else.
The problem here is less that they do not consider if one thing retcons another than it is that they do not think if the new idea is worth it, or what the long-term impact will be.
As much as I like idea-based stories, comics are primarily event driven. But, the more quickly and easily one story over-writes another, the less meaning the events have at even a basic level. (Who cares if Captain America gets shot if he is just going to come back thanks to a magic bullet? I am hard-pressed to think of a single event book that has really mattered. Even CoIE has functionally been over-written.)
How does movie continuity even factor into comic book continuity anyway? There is a huge difference between what those two mediums have to deal with when it comes to continuity....
In terms of changing scenes and pacing, yes. But, the basics of telling a cohesive story are the same in both cases.
You can't just keep telling the stories the same way all the time, you have to be able to change things up once in a while. Just as people grow, change, adapt, so to do characters in these stories.
This is one of the reasons I get so annoyed when the big 2, especially DC, reset everything to just the way it was when....... A friend of mine is reading "Blackest Night", and it is becoming obvious how quickly the multi-colored Corps are going to be forgotten/written out.
I would actually like to see a superhero series written along the lines of "For Better or Worse", where the characters age and occasionally die (from aging). Yes, I know FBOW is has been re-started, but only after over 25 years. The only problem here is that many comic fans do not handle change well. (Yes, this is a stereotype. But, I have seen more than enough evidence to justify it over the years.)
So far, Enterprise was the only one that I can recall that blatantly out and out contradicted continuity and one could even argue that the way it ended effectively explains any contradiction. Heh, that was the best way to end that series. Riker walks out of the holodeck and says "Computer, end program". Etcha-sketch! Whole series never happened!
On the other hand, that would mean viewers just sat through a "dream-sequence". (I am still trying to work out why the proto-Federation did not throw the Vulcans under the Andoran bus when the had the chance.)
This is actually in response to my bit in the AHM thread about how Megatron is acting different towards Starscream in AHM than he did in Infiltration. I pointed out how this is a similar case to what happened in the live action movies--in ROTF, a lot of people were surprised at how Prime was openly willing to just go and action hero murder Decepticons, which differed both with how Prime is usually portrayed and partially with the '07 film. (Prime still murdered Bonecrusher without a second thought, but he seemed to be more forgiving when it came to Megs, I thought.)
Killing Bonecrusher, (and in some drafts, Barricade), was justified.
I was less annoyed that Prime and co killed Demolishor and Sideways in the second movie than with how they did it. Prime's "Dirty Harry" moment put the movie an example of unintentional self-parody.
The regret he showed after Megatron died, (even though Sam is actually the one who killed Megatron), is likely the result of bad editing and using a scene from a draft that kept the "Prime and Megatron are brothers" plot.
