Feature request from mage2pro, posted on GitHub Nov 20, 2015
As I understand, the preference
should be avoided, and in 99% cases a usage of preference
is an extension's developer fault (a lack of skill with plugins, observers, and other techniques) and in the remain 1% cases it is Magento 2 core fault (for example, if the problem core method is static or protected and there is no other way to change the system behaviour, see https://github.com/magento/magento2/issues/2265#issuecomment-154351312 and https://github.com/magento/magento2/issues/2202#issuecomment-151599087).
Anyway, I think, the system should warn the administrator that the installation could break other extensions.