There is an amazing idea brought down in the 1st section of the Ramchal's Mishknei Elyon, which discusses the secrets for the 3rd Beit HaMikdash.
It is written in Tehillim 122:3
ירושלים הבנויה כעיר שחברה-לה יחדו
Yerushalayim, built as a city that was connected together.
According to the sod, this refers to the fact that there is an Upper (spiritual) Yerushalayim and a Lower (physical) Yerushalayim.
Originally, the Upper Yerushalayim (namely the Beit HaMikdash) was built in one fashion, and it was this fashion that Shlomo HaMelech copied down below, and therefore the Upper and Lower Yerushalayim was in synch.
When the 1st Beit HaMikdash was destroyed, however, the "design" of Upper Yerushalayim immediately changed. This is the sod of what Yehezkel saw in his vision. It was not a vision of the future alone, but also a vision of the present, but on the spiritual plane alone.
When the Upper and Lower Beit HaMikdash "match", the Shechinah dwells in the Beit HaMikdash. For this reason, the Shechinah did not dwell in the 2nd Beit HaMikdash, which had elements of both the 1st Beit HaMikdash and Yehezkel's vision mixed together.
When the zivug occurs (which would be upon reaching the level of Ateret HaYesod), The Upper Yerushalayim will "come down" in a spiritual fashion, and around this, Am Yisrael will physically construct the 3rd and final Beit HaMikdash, wherein the Shechinah will again rest.