Or HaChaim on Genesis 49:28/אור החיים על בראשית מ״ט:כ״ח

1 כל אלה שבטי ישראל שנים עשר, All of these comprise the twelve tribes of Israel. How exactly is the number twelve made up? Is Levi included? If so, the Torah did not include Joseph as more than one tribe, though Jacob had said to him (48,5): "Ephrayim and Menashe shall be to me like Reuben and Shimon." If Levi is not included in the number twelve, as we find for instance when the Israelites were being counted at the beginning of the Book of Numbers when the flags and positions around the Tabernacle were assigned, why was Levi denied his father's blessing? If the reason was that Jacob criticised him and only those who had received blessings were included in the count, why were Reuben and Shimon included seeing they too had been criticised?

2Perhaps Ephrayim and Menashe were not counted as two separate tribes until after the Exodus from Egypt, whereas here the Torah counts Joseph. I believe this is a rather forced explanation. I prefer to think that the words איש אשר כברכתו ברך אותם, "he blessed them each according to his special blessing," contains the answer to our problem. We note that Jacob included Shimon and Levi in a single blessing. Hence we have Joseph as two tribes and Shimon and Levi as one tribe together making up the number twelve.

3אשר דבר אליהם אביהם ויברך אותם, what their father told them when he blessed them. Although we note that Jacob bestowed no blessing on either Reuben, Shimon or Levi, the Torah makes the point that the very harsh comments Jacob made to these three sons were their blessings. This is why the Torah employs the expression דבר, an expression reserved for harsh words or a harsh tone. The Torah adds ויברך אותם, he blessed them, to make certain we do not misunderstand. When we look at the way Jacob censured Reuben, we are reminded of the Sifri in Behaalotcha according to which the privileges of the firstborn will be restored to them in the future. Inasmuch as Jacob called Reuben his firstborn this was an encouragement for all the firstborn to look forward to the future when they would again be allowed to function as priests. It was on account of that future that Jacob was so intent to acquire the birthright from Esau at the time. The idea that there would come a time when Esau would perform the service in the Holy Temple was anathema to Jacob. This does not mean that in the future these privileges will be denied to the Levites. At the time envisaged both the firstborn and the Levites will share equally in those functions that were performed by the Levites when the Temple was standing. Jacob also blessed Simon and Levi when he cursed their anger. His blessing consisted in that he cursed their excess amount of anger. By reducing their natural tendency to anger he bestowed a veritable blessing upon them. The fact that he decreed that when the land of Canaan would be distributed they should be split up and scattered throughout the land was also a blessing as it would help to blunt any harmful results whenever they would have occasion to display their anger.

4אשר כברכתו according to his blessing, etc. Each person received a blessing in keeping with his individual personality and achievements. You must not forget that different souls possess different potentials. Some souls are able to rise to the level of being priests, others to the level of being kings, etc. Still others have the potential to achieve greatness in Torah knowledge, or temporal successes such as wealth, or personal heroism. Jacob endeavoured to match his blessings to what he perceived to be the nature of each of his sons' special attributes.

5ברך אותם, he blessed them. The Torah uses the word אותם them, (plural) to stress that each and every blessing to each individual son was also meant to be beneficial to the brothers as a whole. When Jacob predicted that Yehudah's hand would be on the neck of his enemies, this automatically meant that Yehudah's brothers would also benefit from his military prowess, etc.