Why did Yaakov name the place 'Beis El' again?
Ramban: He did so a number of times, 1 in order to stress that this location was really and truly the House of G-d, where the Shechinah would always rest. 2
Peninim mi'Shulchan ha'Gra (to 28:19), Ha'Kesav veha'Kabalah (to 28:19): Yaakov called three [different 3 ] places, "Beis El" (28:19), "Kel Beis El" (35:7), and "Elokim Beis El." 4
Oznayim la'Torah: He was duly sanctifying the location as the place where they would ultimately build the Beis-Hamikdash. 5
Ohr ha'Chayim: Now, he called also the place where Hashem spoke to him Beis El, i.e. the city (- Malbim. Initially, he called only the place where he slept Beis El.)
Malbim: He named the current place Beis El for he saw that also it has Kedushah.
Ha'amek Davar: Initially, he called the entire place where he saw angels (ascending and descending) Beis El. Now, he called "Elokim Beis El" specifically to the place where Hashem spoke with him. A Tzadik causes mercy to come to the area he is in, but he brings Din to his precise place; Elokim is Midas ha'Din 6 (but Kel is Midas ha'Rachamim - Rashi to Shemos 34:6).
See Bereishis 28:29.
Ramban: We find the same concept with regard to Be'er-Sheva (See 21:31, 26:33). Also refer to 35:7:1:2 and 35:7:1:3.
Mefarshim on Sefer Yehoshua point to at least two locations named Beis El - one in the territory of Binyamin, and one in that of Efrayim (Yosef). (See "Erkah Shel Eretz Yisrael" by Rabbi Yehudah Landy, p. 31.)
I.e. in this verse, 'Elokim' does not refer to the previous words (to teach that Elokim spoke with him), rather, to the coming words (it is part of the name of the place). (While it might seem that the Ta'amei ha'Mikra support this, in fact the note Tipecha is a bigger stop than a Tevir, putting the words "Asher Diber Ito Sham Elokim" together. (CS))
Oznayim la'Torah: And that was the exact spot that David designated as the Mekom ha'Mikdash, when Hashem confirmed his decision with a fire from Heaven and David declared, "Zeh Hu Beis Elokim!" See Divrei ha'Yamim I 21:26, 22:1.
Harchev Davar: This teaches that wherever a Tzadik is, it is called Elokim, for Hashem is exact with him, with Midas ha'Din.
Why does the Torah repeat the phrase "the location where Hashem spoke with him" three times in the Parshah (in 35:13,14,15)?
Rashbam: Because Hashem spoke with him in an open place, and not in a town.
Oznayim la'Torah (in the name of the Chasan Sofer): It hints at the three Batei Mikdash.
Ha'amek Davar: Initially, he did not know the exact place where he set up a Matzevah 22 years earlier. Now, he knew the place (and set up a Matzevah there). Also refer to 35:15:1:6.
