Why does the Torah refer to the generations of Moshe and Aharon, but list only those of Aharon?
Rashi and Targum Yonasan (in Pasuk 3): Because Moshe taught Torah to the sons of Aharon, 1 and Chazal have taught that 'The Torah considers whoever teaches his friend's son Torah, is considered as if he had fathered him' 2 - Even though he taught all of Yisrael Torah. 3
Ramban #1: Because, having finished counting Yisrael, Moshe is about to proceed with the census the Levi'im, The Torah begins with the leaders of the tribe - Moshe and Aharon.
Ramban #2 and Rashbam: Following the list of the descendents of Yisrael, the Torah is currently concerned with the descendents of Aharon (the Kohanim), following which it will list the descendents of the Levi'im; Moshe is included in "Mishpachas ha'Amrami" (Pasuk 27). 4
See Targum Yonasan (Ibid.) and Na'ar Yonasan. See also Torah Temimah, note 2, DH 've'Hinei'.
See Sifsei Chachamim. Sanhedrin, 19b: 'The Pasuk writes here "ve'Eileh Toldos Aharon u'Moshe" and in the next Pasuk "ve'Eileh Sh'mos B'nei Aharon" to teach us that Aharon fathered them, but since Moshe taught them, they are considered as if he (also) fathered them'. See Torah Temimah, who elaborates.
See Sifsei Chachamim and Oznayim la'Torah.
Ramban and Rashbam: Since, besides Aharon, who is mentioned here, he was the only son of Amram mentioned there.
Why does the Torah call Aharon's sons "Toldos Moshe"?
Refer to 3:1:1:1.
Oznayim la'Torah #1: Because they were destined to die on account of Aharon's sin, and they were spared when Moshe Davened on their behalf. 1
See Oznayim la'Torah DH 'Eileh Toldos Aharon u'Moshe' #2.
Why does the Torah not list Moshe's sons?
Rashbam: Because "Toldos ... u'Moshe" refers (not exclusively to his sons, but) to all the Levi'im - (who are listed later in the Parshah - in Pasuk 15 - and whom Mohe also taught Torah - Oznayim la'Torah). 1
Oznayim la'Torah: Because it is only concerned with the lineage of the Kohanim, and Moshe's sons were not appointed Kohanim.
See Oznayim la'Torah.
Why does the Torah insert the (otherwise superfluous) phrase "be'Yom Diber Hashem es Moshe ... "?
Rashi and Targum Yonasan: Because that is when Moshe taught Aharon's sons 1 and it is considered as if he had fathered them.
Ramban, Rashbam, Da'as Zekenim and Hadar Zekenim: Because, at that stage, before the Mishkan was erected, 2 Aharon's four sons - whom the Pasuk is about to mention - were all still alive. 3
Seforno: Because it is referring to the day on which the tribe of Levi was chosen, some to carry and some to serve Hashem and to bless by His Name (by singing); and on that day Nadav and Avihu were still alive and are therefore included.
Why does the Torah need to insert "be'Har Sinai"?
Rashbam: Because it is referring to the period before the Mishkan was erected, whereas after it was erected, the Torah always refers to it as 'Midbar Sinai'.
