Language should be organic. It should be allowed to evolve naturally without the imposition of artificial "rules of rightness." That being said, good language, like a good garden, is planned or laid out with an eye always toward healthy standards. Some people use phrases -- like others toss chemicals on plants -- without thinking of the harm they're doing. Having said that, I want to to point out that certain phrases have no real purpose in a sentence:
That being said; having said that; after saying that ...
I have several writers whose work I've been editing for a project who seem to use some variation of "that being said" in almost every article, and sometimes multiple times in the same article. I hear correspondents and analysts on TV use some variation of that phrase to help them move to the next point. It's verbage. It's used without thinking, and the way you teach student writers not to use cliches is to help them be aware that when there is no thought on the part of the writer, there is no thought in the reader.
Most of the time when I see the phrase, it doesn't add anything to the sentence it starts. When it does, what the writer really means is "but." I'm not interested in the writer proving to me that he or she is clever enough to be aware of a paradox or is so smart that he or she is about to show why the statement that was just made is not accurate (then why did you make it?). If you mean "but" say "but" and get on with your thought. That's what I want to know--what follows the "but." And if you aren't really contradicting or countering what came before, I don't even need the "but."