Since the Kavana and intention of putting on Tefilin is that we should learn Torah, why is that not mentioned at all in the Yehi Ratzon or any Tefilah in the common Sidurim said before putting them on?

Indeed, Mishna Berura (8: 19) quotes Bach that there are three mitzvos that require an additional special Kavanah or intention when performing them. They are Tzitzis, Tefilin and Suka. In regard to Tefillin the pasuk mentions (Shemos 13: 9): ‘They shall be for a sign to you on your arm, and a memorial between your eyes, so that the Torah of Hashem may be in your mouth.” Horav Shlomo Miller’s Shlit’a opinion is that it is actually included in the words of the Yehi Ratzon said before donning Tefilin, namely: “Sha’ar Chushai Vekochosai Kulam Yiheyu Meshuvodim La’avodoso” So that the soul in my brain – along with all my other senses and powers – be subjugated to His service, and that is achieved by learning Torah.