From Diana Salles:

Whenever I hear “Having said that,” I replace it with “On the other hand”. I wish people could be more honest when they disagree with an assertion. Instead, they say, “Yes there are too many policemen in this neighborhood. Having said that, there aren’t enough policemen in this neighborhood.”

It’s smarmy, too diplomatic.

It ranks with “I hear where you’re coming from” and “More power to you” for misplaced politeness.