And yet, the Ramban, Rashba, Ritva, Rosh and many others did not want people, especially young inexperienced people, to learn it.
The complaints aren’t about the direct Greek quotations. They are about his Taamei Hamitzvos (which don’t show up in the Yad), his explanation of the Merkava, and the implied dependence on the Torah being agreeable to philosophy.
Some have said it is a cloaked Sefer (as he writes himself), which masks even Kabalistic ideas. The Kamarna writes that only someone with an open an holy mind can learn it. Some have said to own but not read it.
It was a great composition to keep hold of a generation and culture that cared very much about certain assumptions and couldn’t accept certain other ideas. Some of these issues are outdated. For example, in a time such as ours in which concepts of machines looking, hearing, knowing, and wanting are common everyday language, we don’t need a whole thesis explaining הנוטע אוזן הלא ישמע. And yet, you still hear people feeling very educated for understanding this.
Why should we instate learning apologetics of a thousand years ago? And yes, our Yeshivos learn Mussar. Some learn Chassidishe Sefarim, and some even learn Sifrei Machshavah. Usually it’s up to the individual.