Over the course of history, both of our Batei Mikdash have been destroyed and looted by our enemies. However, Sforno on the first Pasuk of Parshat Pekudei comments that we never find that any of the vessels from the Mishkan were destroyed or captured by enemies. He offers four reasons for why the Mishkan was so great that its vessels were not destroyed: it was “Mishkan Ha’eidut,” the place of the Luchot of “testimony”; it was commanded by Moshe Rabbeinu, the greatest leader we ever had; the Leviim who served in the Mishkan were under the charge of Itamar Hakohen, who was a great Tzaddik; and the actual construction of the Mishkan was presided over by Betzalel and other Tzaddikim. This last feature differs from the two Batei Mikdash, which were both built largely by foreign laborers. The first was built by men hired from Tzor (Tyre), and the second by men from Tzor and Tzidon (Sidon) commissioned by the Persian king Koresh king. The second Beit Hamikdash also did not have the Aron (it was never found after Yoshiyahu hid it in the times of Bayit Rishon); the Leviim were not present in great numbers in its time (see Ezra Perek Chet); and it was commanded to be built by Koresh, a foreign king. The Batei Mikdash were thus lacking in many of the special qualities of the Mishkan, giving the Mishkan much more Kedushah than either Beit Hamikdash.
Sforno makes a similar comment at the end of Parshat Nasso. He asks why the Torah felt the need to recount the whole combined value of the gifts of the tribal leaders; after all, we can do the math on our own. He answers that it is to be contrasted with the first Beit Hamikdash. The Torah in Nasso says immediately after the account of all the leaders’ gifts that Moshe came to the Mishkan and was able to speak to Hashem. This is different from the times of the first Beit Hamikdash, when absolutely no one could simply walk into the Beit Hamikdash and speak to Hashem. Even though the Korbanot brought at the inauguration of the Mishkan were very few compared to those brought at the inauguration of the first Beit Hamikdash, the Mishkan was so much holier that Moshe could enter and speak to Hashem whenever he felt the need. The quantity was insignificant, but the quality was much higher. This may be why so many Pesukim of the Torah are devoted to the establishment of the Mishkan.
Clearly, then, the Mishkan represented a special, unique phenomenon, a level of Kedushah that history has never seen since.