Please do not re-enable alerts or provide an option to enable default alerts when upgrading.
After upgrading we have received close to a hundred emails due to a default alerts being re-enabled.
Which alerts in particular became re-enabled after upgrade? Alerts which are deleted will be recreated with their default configuration whenever the Configuration Wizard is run. However, if you've modified an alert, such as in the case of disabling it, upgrading or re-running the Configuration Wizard should not re-enable those alerts.