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and the update-function is to bad. The users like the function and upload all files, incl files screenshit and many language-files.
No visits for a update or read the history :(
Out of the options presented: I'd like an intermediate plugin that hijacked the "Right Now" widget on the dashboard to let me know about the coming changes or hijacked the "upgrade your WordPress" yellow warning-box-thing. Maybe with an ajax-y close-this-window checkbox?
Personally I wish the upgrade process would pause once it has downloaded the zip file and display the readme file (and / or perhaps a changelog file) - and only resume installation once the file has been scrolled through / read and a button pressed.
Having a link to the readme file of each plugin on the plugin page might also be quite useful, and I think I have seen a plugin that does that (and more) - but I can't remember the name of it.
What I mean is that the people who automatically upgrade without checking the code are not likely to have checked the code even without the automatic update, so probably the only thing that has changed with 2.5 is the likelihood that users will upgrade, not their degree of caution.
But to answer your question, if breaking upon upgrade were unavoidable, I think I would check for the existence of the earlier version and then disable the main functionality, with a prominent admin area warning (like Akismet's "you don't have an API key" message). Then the user could opt in to the breakage, or (by following a link) re-install the previous version.
Out of all the options I personally favour including an older version of the plugin which is enabled automatically, but which has an added page for the user to trigger the replacement.
I may be trying this out fairly shortly on my fun with sidebar tabs plugin because I need to change the class based system to an ID based system and I want to change the structure of the html. There could be a fair amount of breakage.