I will add a wish list item for it in the project tracker but not sure when I will get to it, I view it as a nice to have but not a high priority.

For a single site installation one could customize them and then restore their custom versions after upgrades.

If/when I would get to something like this I'm not sure I would try to make a global solution for all message templates because they are used in a wide variety of contexts, so it might be more effective to request specifically which templates you would like to be able to customize on a per site basis.

Best,

Joe