Before Yaakov dies he calls Yosef and tell how his two sons, Menashe and Ephraim will be like Reuven and Shimon. This is viewed as a double portion for Yosef because his two sons will produce tribes as great as Reuven and Shimon. Rashi says that all future sons of Yosef will be included in either Ephraim or Menashe. Rav Samson Raphael Hirsch commented that all of Bnei Yisrael are trying to fulfill Hashem’s mission in the world. However, they are divided into twelve tribes since the Jews represent many aspects of life. Yosef is special because he produces two tribes, which will each embody a separate character trait to bring the world closer to Hashem. Therefore, Rashi is saying that even if Yosef has many more children only Ephraim and Menashe will stand out by having their own characteristics.
Therefore, Yaakov could be giving Ephraim and Menashe the Bracha of attaining the potential that Reuven and Shimon should have had. Reuven and Shimon were two of the most disappointing tribes. They, along with the tribe of Levi ruined many opportunities to be the leaders of Yisrael, and in the end, Yehuda received royalty. Chazal teach that Reuven moved Bilha’s bed, and Shimon suggested the murder of Yosef, and as a punishment, the populations of both tribes were ravaged during the plagues in the Midbar. Majority of the tribe of Reuven were killed out after blaming Aharon for the death of Korach, and majority of the tribe of Shimon were killed because of the sin of Baal Paor. Further, both tribes were ultimately estranged from the rest of the nation. Shimon only received a small portion of land below Yehuda’s portion, and Reuven was on the far side of the Yarden.
Throughout Tanach there is a recurring theme of younger brothers accomplishing more then their older siblings. This shows that ones owns effort will directly affect his success. Since Yosef used his life to the fullest by passing tests and making a Kiddush Hashem he was given two tribes who would accomplish together twice as much as any other shavet.