Why is the Counting of the Omer so important?

The Ramban (Leviticus 23, 31) explains that the purpose of counting is to connect Pesach to Shavuot, thus creating, so-to-speak, one ongoing holiday spanning the 49 day count. Pesach represents the first Yom Tov of the holiday, Shavuot – the last, and the days counted in the interim are parallel to Chol Hamoed.

Why is it so important to connect Pesach and Shavuot?

Beyond the spiritual aspiration expressed by the counting, one can find another reason underlying this Mitzvah.

We find a disagreement (Menachot 65-66) between the Boethusians and the Pharisees regarding the term, "from the day after the Sabbath." The Boethusians believe this refers to the ordinary Shabbat within the Pesach holiday (Shabbat Breishit), implying the counting must begin on a Sunday. The Pharisees, on the other hand, interpret this term as the day after the first Yom Tov of Pesach. This dispute has additional Halachic ramifications. According to the Boethusians, it is not possible that the day of the harvesting of the Omer will be on Shabbat, since it must always take place "the day after" – Sunday. However, according to the Pharisees, if the first day of Pesach falls on a Friday (this was a possibility at the time the new month was sanctified by visual verification), the harvesting of the Omer would indeed take place on Shabbat (Menachot 63-64).

HaRav Kook zt"l (Maamarei Hare’iya 179-181) elucidates this legalistic dispute based upon the principle ruling that an individual’s personal sacrifice does not override Shabbat, while a public offering can override Shabbat. The disagreement between the Boethusians and the Pharisees was not over the sanctity of Shabbat – "The Boethusians were certainly not more concerned about the sanctity of Shabbat and its integrity than the eternal keepers of the Torah – the Pharisees. Their battle was not waged over protecting Shabbat from desecration by the harvesting of the Omer." The crux of the argument was between opposing views regarding agriculture in the Land of Israel:

The Boethusians considered agriculture in the Land of Israel as a private economic matter, in order to provide sustenance and a livelihood. As such, it does not override Shabbat.
The Pharisees point of view saw agriculture as "imbued with holiness, and this holiness is at its very foundations, highlighted by the celebration of the first harvest, the Omer, rising to the highest level of holy worship – and the offering is a public sacrifice which overrides Shabbat."
In other words, agriculture in the Land of Israel emanates from a wellspring of holiness, and is intrinsically linked to the role of Am Yisrael. Therefore, the celebration of the first harvest is a celebration of the entire people, and overrides Shabbat.

That being the case, the Counting of the Omer represents two distinct processes of holiness: a spiritual process beginning at the exodus from Egypt and culminating with the Revelation at Sinai, and an agricultural process, which reflects our thanks for all our grain and embodies the recognition of the unique holiness of the Land.

It then becomes clear that the Counting of the Omer has a special connection to the Land of Israel. We are privileged to be in our Land, to dwell in Eretz Yisrael!

For many generations, our ancestors could only find expression of the spiritual process of the counting of the Omer, which is linked to Matan Torah on Shavuot. Although we still do not have our Temple and we do not bring the offering of the Omer and Shtei HaLechem on Shavuot, we have been privileged to live and dwell in our Land. Our spiritual advancement during the days of the Omer is related to the Land of Israel. While this link is particularly emphasized in relation to the agricultural realm, it is present in all the realms of human development and creativity in our Land (Chatam Sofer, Succah 36; Minchat Aviv, page 113). Out of the holiness of the Torah, we can connect the sacred and the mundane. This connection is most profound in our Holy Land, where the materialistic world, in general, and the agricultural world, in particular, are raised to a level of holiness.