Several notable points surface upon reading Ya'akov Avinu's blessings to Ephraim and Menashe. Firstly, Ya'akov initially requests of Yosef, "take them to me and I shall bless them" (48:9), but later the verse states, "And he blessed Yosef and he said... The angel ... shall bless the youths" (ibid. 15-16). Following that, the Torah records another blessing, "And he blessed them saying, 'With you (becha in the singular) shall Israel bless, "May G-d make you like Ephraim and Menashe"'..." (ibid. 20). The Torah seemingly alternates between the blessings being directed toward Yosef and their being directed toward his children. Furthermore, it is noteworthy that the first blessing does not mention Yosef's children by name whereas the second one does.
The commentaries present different approaches resolving one or more of the above anomalies. Ramban explains that the first blessing was a blessing to Yosef since the greatest blessing a father could receive is a blessing for his children. He similarly explains the usage of the singular "becha" in the second blessing: Ya'akov was telling Yosef, "The Jewish people will use your descendants as paradigms for their blessings". Ohr HaChaim and Seforno explain that Ya'akov at first separately bestowed a blessing upon Yosef the content of which is not described and then proceeded to bless Yosef's sons, Ephraim and Menashe. Alternatively, Ya'akov first bestowed the power of blessing - which had been given to Ya'akov from his father Yitzchak who, in turn, received it from his father Avraham - upon his beloved son Yosef, and then Ya'akov proceeded to bless his grandchildren.
Abarbanel, in explanation of the need for two blessings, comments that the first blessing was for both children equally. He notes that there are three different types of blessings: for spiritual success, for physical success and for protection from harm. Ya'akov Avinu blessed his grandchildren together with all of these in the first blessing. (See there for the detailed explanation.) The second one highlighted their names indicating each one's uniqueness. Rashi notes that different types of leaders emerged from each tribe. Netziv (see also Rav S. R. Hirsch) stresses the fact that Ephraim excelled in spiritual matters; Menashe excelled in the worldly qualities of leadership and court conduct.>[1] A blessing is designed to augment the qualities and talents with which one was already endowed. The blessing used by the Jewish people thus wishes upon the person being blessed that he excel in the particular quality that is already present within him. Based on this concept, he explains the cryptic statement of Targum Yonasan (Yerushalmi) that this blessing would be used at a bris milah.[2] It is at that early stage in the child's life when his qualities are not yet known that the dual blessing of being like Ephraim (excelling in the spiritual) and (or) like Menashe (excelling in the physical) is appropriate.
Mikdash Mordechai (quoted in Talelei Oros) offers an alternative explanation why the sons of Yosef are uniquely chosen to be the models of blessing. They were the first brothers in Biblical history known not to be envious of or quarrelsome with each other even after their grandfather placed the younger Ephraim before the elder Menashe. His comment is especially meaningful in light of the Netziv's comment that they were quite different from each other, a fact that oftentimes, unfortunately, leads to enmity and strife. Fathers bless their sons that they should excel in their unique qualities but also admire and respect the unique qualities of others.
In closing, a comment by Be'er Yoseif by Rav Yosef Tzvi Salant is most worthy of mention. Yosef, as the viceroy of Egypt, had unlimited resources to rear his two sons to excel, each with their own unique talents: Menashe as an officer in the palace and Ephraim as a devoted student of his grandfather Ya'akov. How could a "pashute Yid" with limited resources have hopes that his children will excel? For this reason, Ya'akov Avinu used the singular "becha" introducing the second blessing referring to Yosef himself. In effect, he was saying that the Jewish people will learn from Yosef's miraculous rise to success both spiritually and physically after being sold as a slave, accused of crimes by his master's wife and imprisoned for twelve years! With Hashem's blessings and providence, nothing is impossible. May we all merit blessings from above and respect each other's unique qualities thus emulating the unity of Ephraim and Menashe.
[1] See Priority and Innovation, by Mori v'Rabi Rav Mordechai Willig shlit"a, for further elaboration of the Netziv's approach.
[2] For another approach, see Invest in Futures - G-d Does, by Rav Benjamin Yudin shlita.