The Counting of the Omer is intended to bring about a revelation of the “50th Gate of Understanding”. This level will be revealed in a complete and permanent manner in the Era of Geulah (Redemption).
From the Rebbe’s explanations:
– Directly after the Counting of the Omer, we recite “Yehi Ratzon” – a special prayer asking G‑d to rebuild the Beit HaMikdash. It is explained that at present, our Counting of the Omer fulfills merely a Rabbinic command, instituted as a commemoration of the service in the Beis HaMikdash. In the Era of Redemption, the mitzvah will again have the status of a Torah command. Therefore, after fulfilling the mitzvah, we ask to be granted the opportunity to fulfill the mitzvah in a complete way.
Although the Rabbis instituted many other mitzvos in commemoration of the service in the Beit HaMikdash, we generally do not conclude them with a prayer of this kind.
The Omer Count is different. There is an intrinsic bond between the ultimate redemption and the Counting of the Omer.
And it’s this connection that the “Yehi Ratzon” prayer comes to reinforce.
From the Rebbe’s talk on the Acharon Shel Pesach, 5751 (1991). Free translation.