I was always a fan of upgrades, but in the meantime I am more a follower of:
"If you upgrade to this new version, please re-setup your whole wine configuration and merge over your data."
This should only very seldom be the case anyway.
This causes less work for us and less work for the user due to us breaking his update.
It does rather discourage us from making improvements to the Wine configuration that could improve compatibility though, because everybody hates the hassle of upgrading and 99% of users will forget anyway. So, I think there's value in making it automatic.
thanks -mike