Why does it say that Yaakov called it Beis El? It was already called so in the days of Avraham (Bereishis 12:8)!
Sechel Tov (19:19): People used to call it Luz. 1 The Torah called it Beis El, for later that would be its name, just like "Sedei ha'Amaleki" (see Rashi to 14:17).
Rashbam: Due to where Yaakov slept, they changed the name of the city to Beis El.
It says here that Yaakov called it Beis El. Below (35:6,7) it implies that he called it so only when he returned!
Tosfos ha'Shalem (4): Yaakov slept outside the city, and called the place Beis El. The city was called Luz. Malbim - He changed the name of the city to Beis El only later.
Ha'amek Davar: Later the city widened, and included Beis El, and the entire city became called Beis El.
"Yaakov referred to the Beis ha'Mikdash as a Bayis... [calling it] Beis-El" (Pesachim 88a). Why did specifically Yaakov refer to it by this term?
Maharal (Netzach Yisrael, beg. Ch. 52, p. 196): Avraham's trait was Chesed, and Yitzchak's was Din. Though these traits, they brought about a connection between Hashem and the physical world; and the place of that connection is the Beis ha'Mikdash. Avraham referred to it as a mountain; its great size symbolizes Chesed. Yitzchak called it a field, which is straight and level, like Din. Yaakov's trait is Rachamim (mercy), meaning love and synthesis, and he called it a Bayis (home). The types of connection represented by a mountain or field can be annulled, whereas that which is portrayed by a home cannot be. 1
I heard it explained that Avraham and Yitzchak possessed traits by means of which they arrived at attachment to Hashem, whereas Yaakov's trait was the attachment itself. Through this trait, he merited the other traits as well. (EK)