Student or Learner
Does the sentence: I wish you were here mean the same as It's a pity you're not here?
I really don't think so.
Maybe it's a pity for ME if I wish you were here, but "it's a pity" carries a sense of sorrow about the overall condition of things, compared to "I wish," which just expresses a desire that isn't met.
One person might say, "I wish we could have ice cream for breakfast" but a nutritionist would not agree that it's a pity he didn't!