While it is true that Jesus wasn't thinking primarily of you or I during his earthly ministry, John 17 is an example of an eye on the future. Jesus wanted Israel to repent and take the gospel to the world. In his 12 disciples, he had a new Israel that would be made out of Jews, and later Gentiles (non-Jews). And wanted them all to be united.
John 17 is part of Jesus' final discourse, a section I love. We learn more about the Triune nature of God there than anywhere else, and discover how it includes us.
Verses 6-19 are missional; a prayer for the disciples to be in the world (human society) but not of it (shaped by non-gospel cultural norms). Sanctification, or the process of being set apart for mission, is in the the word of God, which are truth. Jesus himself is truth, so ultimately the word is about Jesus. The mission is the gospel of Jesus, the preparation for mission is the gospel of Jesus.
He then shifts to those who would believe because of the word of his disciples, that we may be one. United. Just as Jesus in the Father and the Father is in Jesus. The Trinity (early, Jesus spoke of the Spirit) is a model for Christian community. Sure we remain physically and metaphysically distinct, but in purpose and community. This is meant to be a witness to the world. In the first century the church's unity was radical, with women treated as equals, slaves and citizens eating together, Jews and Gentiles associating.
Now I know what it is to fellowship with people with different theological views, and yet try and focus on commonalities and mission. There are times to discuss, times to differ, but many more times to join in mission for Christ's sake. Let our unity, Trinitarian in shape, be what defines us.