Today there is no easy way to apply an override to enable/disable rules, or perhaps to change priority on alerts for all rules across all Management Packs given the current toolset. You have to purchase a 3rd party tool like MPStudio from SilectStudio to do so. Please provide enterprise ready authoring capabilities to override common parameters for rules/monitors across 1 to many Management Packs that are selected. Look at the way MPStudio allows you to manage bulk overrides for an example.
When deploying SCOM and tuning the environment, this is an absolute must.
It would be nice to have this functionality available through a GUI, but adding powershell cmdlets might be acceptable as well.