"I wish it was you"- the speaker wanted "it" to be "you", but it can't be a reality- the speaker is just being wishful. One could say this in many situations, one of which is "someone is at the door, and the speaker goes and opens the door, finding it is NOT someone he was expecting, it is now that the speaker could say this to himself "I wish it was you, but alas, it wasn't you" Another example, I wish I were you - this can't be true of course, as someone can't literally be someone else; it just means, the speaker(in a way, admires someone), and wants to be as good as someone else as is. The other sentence there, the following, is incorrect.
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"I wish it was you"- the speaker wanted "it" to be "you", but it can't be a reality- the speaker is just being wishful. One could say this in many situations, one of which is "someone is at the door, and the speaker goes and opens the door, finding it is NOT someone he was expecting, it is now that the speaker could say this to himself "I wish it was you, but alas, it wasn't you"