I wish you were here with me. Present tense. This can only be spoken in the present, as a wish for the present, but the sentence uses the past tense form of the verb 'to be'.
I wish you had been here with me. Past tense, expressing a situation that you would have wanted at some point in the past, but couldn't have.
I wish you were going to be here with me. Future tense, expressing a situation that you want in the future, but can't have.
The above are actually all examples of the 'past unreal tense', as for present, past and future situations, a past-tense form of the verb 'to be' is used.
Native speakers of English say these things quite naturally, of course, but most of us find it very difficult to explain, as the term 'past unreal' does not always seem logical. Even native speakers of English sometimes find the verb forms in sentences like this difficult to get right.