When sub sites have different permutations of plugins activated, I miss the ability to toggle the activation state for a plugin when updating it. For instance:
Site A has plugins X and Y
Site B has plugins Z and Y
Site C has plugins X and W
Assuming that X needs updating, it would then be nice to be able to deactivate X, update it and reactivate it without Site B suddenly getting X. Today I have to make a note of which sites uses X, and deactivate/reactive it manually - at least I think I do.