"Were" is the subjunctive. I think it comes to English from the German subjunctive form "wäre". It's not the same word as "were", as in "We were running".
The example you've chosen refers to an event in the past, so "were" seems to be ambiguous in that context, because it could be "you were there", prefixed by I wish - i.e. the writer isn't trying to use the subjunctive at all, which I think is nowadays OK.
"I wish you were here" is a clearer example. That is clearly present subjunctive. "I wish you had been here" would be referring to an event in the past - so that's some kind of past subjunctive.
The example you've chosen refers to an event in the past, so "were" seems to be ambiguous in that context, because it could be "you were there", prefixed by I wish - i.e. the writer isn't trying to use the subjunctive at all, which I think is nowadays OK.
"I wish you were here" is a clearer example. That is clearly present subjunctive. "I wish you had been here" would be referring to an event in the past - so that's some kind of past subjunctive.
I regret the death of the subjunctive.