In my video, "Should Every Jew Move to Israel", I explained that all of our prayers from all over the world first come to the Kotel and from here they go on into Heaven.
Joshua commented, "Great Video! One correction…all prayers go to the Har Habayis (the Temple Mount) before ascending, not the Kotel…"
As often happens, there is disagreement between our sages. Apparently, the great majority of rabbinical authorities except the Rambam say that the holiness of the Temple Mount ceased either after the First Temple was destroyed or certainly after the Second Temple was destroyed.
Even though the vast majority of those sages say there is no remaining holiness on the Mount, still we say, just in case the Rambam was right, we are not to go up onto the Temple Mount until the Moshiach comes and then we will all be able to go up again.
The Kotel was not even part of the Second Temple. It was "merely" a retaining wall built to guard the Temple Mount from sliding and thereby weaken the Temple's foundation. Today's holiness of the Kotel is not due to its original function. A Midrash tells us that the Kotel was built with the funds gathered from poor Jews' charity. This is why it was not destroyed with the Temple. But its special place in the spiritual world today is because the Shechina (G-d's revelation) never leaves the Kotel. This is why our prayers come to the Kotel first and from here they proceed to Heaven.
When the Temple was standing all of our prayers came to the Temple Mount and then went on into Heaven. And when the Temple will be rebuilt (soon in our day) again our prayers will come to the Mount and from there continue on up into Heaven. Now we have the Kotel. We thank G-d for what we have, and we pray that He will soon bring the Temple.