In 46:3, Hashem tells Yaakov, אל תירא, “Do not fear.” Yaakov was about to see Yosef, his long-lost son, and he was going to live in Egypt under the protection that Yosef would grant him as second to the king.
In Parshat Toldot (26:2), Yitzchak was told by Hashem to stay in the land that Hashem gave him and specifically not to travel to Egypt. This could be what Yaakov was afraid of: that his journey would violate Hashem’s command to Yitzchak. The Abarbanel says that Yaakov had no real fear of going to Egypt: Yaakov did not want to violate Hashem’s command, and this was manifested in his fear of leaving the Jewish homeland and entering Egypt.
The Chizkuni says that the phrase אל תירא means that Yaakov was truly afraid of going to Egypt. Hashem told the Avot that their descendants would be slaves in a foreign land. This is why Yaakov was afraid, but Hashem reassured him that in the end Hashem would bless Yaakov and make his children a great nation. Yaakov realized that his children would return to Eretz Yisrael, but he thought that there was no guarantee that the Jewish People would want to leave Egypt.
Rashi says that Yaakov was bothered by the fact that he was obligated to leave Eretz Yisrael, but the Zohar comments that Hashem assured Yaakov that he would be returned to Eretz Yisrael to be buried with his ancestors.
The Ibn Ezra says that Hashem told Yaakov that he would be with Yosef again, and Yosef would “place his hand on your eyes.” This refers to someone who closes the eyes of someone who is dead. The Or Hachaim elaborates that Hashem told Yaakov that Yosef would outlive Yaakov, showing that Yaakov did not have to worry about Yosef’s death.
Later in this Perek, Yaakov and Yosef meet. The Torah says that he kissed him, but it is unclear who kissed whom. Rashi says that Yosef kissed Yaakov, and Yaakov did not kiss Yosef. Chazal say that Yaakov was reciting Shema. Ramban quotes this opinion as well, but he begins by saying that the phrase “and he appeared to him” means that they saw each other. While Yaakov was getting older and his sight was getting weaker, Yosef was wearing a turban, as was the custom of Egyptian kings, which was covering his eyes. Who kissed whom remains unclear. The Ramban might be the stronger opinion, but there is a psychological element involved: who is more likely to cry? An elderly parent who has not seen his son for a long time or the son who is second in command of a world power?
When Yaakov and Yosef drew closer to each other, they were able to see each other more clearly and then one cried on the other’s neck. Because the Pasuk uses the word עוד, “more,” perhaps Yaakov cried, as he had been crying for twenty-two years. Rashi thinks that the word עוד refers to Yaakov, but he cites a verse from איוב to show that עוד does not always mean “more,” and at times it may mean “much.” This lessens the impetus to say that Yaakov was the one who cried.
The Be’er Yitzchak explains that crying is not something that Yaakov would have done at a time of happiness. The greatest love that one must have is the love for Hashem. Yaakov was extremely happy when he was reunited with Yosef, and this happiness almost went beyond the absolute love that he was supposed to have for Hashem. Yaakov was very careful not to forget the absolute love he had for Hashem. This may explain the Midrash that says Yaakov was reciting Shema when he met Yosef. As Yaakov was reuniting with Yosef, he recited the Shema in order to concentrate on his absolute love of Hashem.
Perhaps Yaakov’s tears were not tears of happiness but rather tears of concern for the future of the Jews in exile in Egypt despite Hashem’s consolation. This exile could lead to assimilation and immorality. One other opinion is Rav Hirsch, who says that Yosef was the one who cried. Even after Yaakov stopped crying, Yosef continued to cry on Yaakov’s shoulder. While Yaakov spent the last twenty-two years mourning for Yosef, Yosef spent many of those years with great wealth. Meeting Yaakov reminded Yosef of the time he spent with his father, and these feelings made him cry more than Yaakov. In short, Hashem’s Torah reflects real life — it contains many ambiguities and complexities.