"I wish you were here" -- in this location, now or in the past. "I wish you were there" -- at another location, now or in the past. "I wish you had been there

"I wish you were here" -- in this location, now or in the past. "I wish you were there" -- at another location, now or in the past. "I wish you had been there" -- at another location, in the past. "had been" means that the action is concluded. "were" is for both continuing and concluded actions, and more words are necessary to glark it from context.