The key to understanding Shavuos is in understanding its names. Shavuos has a number of names, and each of them highlights one aspect of the Holiday and its observances.
Wheat is the latest grain of the year.
The reaping season concludes with the reaping of the wheat, which takes place around Shavuos time, as we mentioned above. Every farmer would bring to the Holy Temple the first ripe fruit of each of his crops. Not all his crops, mind you. The Two Loaves were also part of the First Fruits Offering, except that they were brought by the Kohanim. The Two Loaves would be baked from the fresh wheat crop that had just been cut.