My first reaction to "it is what it is" -- it's an entirely vacuous statement -- of course everything is what it is --what else could it be but what it is?

In its best sense, I think it means "I'm not going to characterize it or put a spin on this" which suggests honesty and acceptance.

My ex used to say it to mean it as "I don't have any control over this" with the subtext "I reject the idea there's something I can do about this (whether I can or not) so don't ask for any solution from me."