Why did Yaakov say "He'asefu" (49:1), and also "Hikavetzu"?
Da'as Zekenim (to 49:1): This hints that twice they will be exiled and gathered.
Malbim: Kibutz is gathering scattered things, and Asifah is (taking inside what is now outside) after Kibutz. He told them to become one Asifah without arguments, to prepare themselves for redemption, as Yechezkel illustrated (Yechezkel 37:16-17, 21). He was to take two sticks (representing Yehudah and Efrayim), and Hashem would fuse them; thus Yisrael would return to their land. Yaakov wanted to reveal the deadline for redemption. The Shechinah left him, for there would be feuds among them, so he told them to make a Kibutz.
Malbim, citing a Midrash: "He'asefu" applies to the 10 tribes, and "Hikavetzu" applies to Yehudah and Binyamin - "v'Asaf Nidchei Yisrael, u'Nefutzos Yehudah Yekabetz" (Yeshayah 11:12). The 10 tribes are not scattered, only that their place is not known; so Asifah is needed, i.e. taking inside what is now outside. Yehudah is scattered all over the world; they are not Nidachim, for their place is known. Whenever verses contrast Yehudah and the 10 tribes, they are called Yisrael and Yaakov, respectively.
Ha'amek Davar (to 49:1,2): Asifah is gathering special people for a purpose, and not a general Kibutz (gathering). He wanted to his sons to come close to his bed, for a Berachah works better when the one blessed is in front of him. Kibutz is the entire nation of Yisrael to some special place, e.g. "b'Za'akach Yatziluch Kibutzayich" (Yeshayah 57:13) - a gathering and Tefilah of the Rabim in some place that they pray. All of Bnei Yaakov (i.e. the entire nation) could not come close to his bed! Yaakov commanded that they later gather to a spacious place, to hear from Yaakov's sons what he had told them.
Why did Yaakov say "v'Shim'u" twice?
Tosfos ha'Shalem (11) 1 : When Yaakov felt that the Shechinah departed (refer to 49:1:1:1), he was worried that there is a Pesul in his children. The extra "v'Shim'u" hints that we should expound it. The middle of the word forms the word 'Shema,' and the initial and final Vav allude to six words that they said (Shema Yisrael...), and six that Yaakov responded (Baruch Shem...), in all 12 (i.e. all 12 sons are Kosher). 2
Malbim: One corresponds to the 10 tribes, and one to Yehudah; refer to 49:2:151:3.
Ha'amek Davar: The latter means to accept the matters.
Why did he say "El Yisrael Avichem"?
Ha'amek Davar: There are two reasons why you should accept my words. (a) I am Yisrael, speaking with Ru'ach ha'Kodesh 1 (close to his death, even though in Egypt, he was normally called Yaakov). (b) I am your father - you should accept my decree and counsel.
Refer to 47:28:150.1:1; and 48:2:151:1.