Rashi: The great leader Gid'on would descend from him, through whom Ha'Kadosh-Baruch-Hu would perform a great miracle.

Malbim: Quantitatively (his tribe would be more populous than Efrayim). This is via nature, which corresponds to the left hand. ¹

Rashi: Because Yehoshua would descend from him, who would distribute Eretz Yisrael to Bnei Yisrael, and teach them Torah. ¹

Targum Yonasan: Even though Menasheh was destined to become a populous tribe, Efrayim would eventually become even more populous.

Malbim: Qualitatively. One person can equal an entire nation, due to his level and Kedushah. (R. Akiva expounded ² that one woman gave birth to 600,000; i.e. through Moshe, who was equal to all of Yisrael.) The greatness of Efrayim is above nature; it depends on miracles that will be done via Yehoshua. Therefore, Yaakov blessed him with the right hand. Also, it is immediate (the aptitude is already there). Menasheh's attribute (numerical increase) will come only later.

Ha'amek Davar: He will be more honored - therefore, he needs the Berachah with the right hand, for extra influence.

Rashi: Yaakov was hinting here, not to the people, but to the actions of Efrayim's descendant Yehoshua, ¹ whose fame ² would spread world-wide, when he caused "the sun to stand still in Giv'on and the moon in the valley of Ayalon" (Yehoshua 10:12).

Targum Onkelos: What Yaakov meant was that Efrayim's descendants were destined to rule over nations.

Targum Yonasan: He meant that Efrayim's descendants would be (more populous than those of Menasheh, and that they would be) populous among the nations. ³

Malbim: One of Efrayim's descendants (Yehoshua) will be equal to many nations.

Ha'amek Davar: Yehoshua, from Efrayim, was very great in Torah, even before the led the nation. He was the father of Torah She'ba'al Peh in his time! "Zar'o" includes his Talmidim, for one who teaches another person Torah, it is as if he gave birth to him (Sanhedrin 19b); all of Yisrael were his Talmidim! The Pilpul (investigative analysis) of Torah and depth of Halachah were widened when Yisrael went to exile. All Ba'alei Talmud were Talmidim of Yehoshua. Yaakov said specifically Zar'o (and not Hu, i.e. Shevet Efrayim), for Yehoshua's wondrous power of Torah did not remain in his Shevet; rather, in Levi and Yehudah. ⁴

Ha'amek Davar: Initially, Yaakov was immersed in intent of the Berachah; he did not [verbally] answer, but he refused to remove his hand. After he blessed them, he told him the reason.

Harchev Davar: Even if he erred, we do not demote one who was aggrandized mistakenly (in this case, he received a greater Berachah). If a great Chacham received Semichah [even based on a misunderstanding], he keeps it (Sanhedrin 30b). If a Talmid gives a bad reason for Zechus, he stays with the judges the entire day, lest his elevation cause his decline (ibid., 42a). Afterwards, Yaakov gave his reason.

Ohr ha'Chayim #1: This refutes the first possibility that Yosef considered. ¹ I know that surely, you (as my son) do not esteem your own right over mine, and you put the Bechor on my right!

Ohr ha'Chayim #2: I know your claim [that favoring one son over others led to Galus Mitzrayim]. I know that it was due to Beni (your dreams and words)!

Ha'amek Davar: I know that you, my son, have intellect to arrange [your sons] so Menasheh will be to my right!

Ohr ha'Chayim #1: He refutes the second possibility that Yosef considered. (b) If you question why I withhold my right hand from the Bechor - it is not because Menasheh is at a low level. He too will grow to be a nation! My right hand is on Efrayim due to Yehoshua, who will come from him. Presumably, the potential for Yehoshua was already in Efrayim, even before Yaakov's Berachah!

Ohr ha'Chayim #2: I know from Nevu'ah that the younger will surpass the older. I cannot oppose what Hashem wants!

Pri Tzadik: Do not think that I do not consider Menasheh to be the Bechor, because I think that you had fathered a child through Eshes Potifar. ¹ When you [were about to sin with her, and you saw my image, ² also I saw, so] I know that you fled.