Rabbeinu yonah’s regret over his machlokes with the rambam wasn’t in his opposition to the shita itself, but rather in that he did not, in his understanding, give proper kovod to the rambam. Nowehere in shaarei teshuva does he advocate philosophy. The amount of other rishonim who argued with the rambam were copious…see the hakdama lf yam shel shlomo for some very, very strong words from the maharshal, who was an early acharon. To see a wide array of sources regarding the mesorah’s opposition to philosophy and “rationalism”, see the lev tov’s introduction to chovos halevavos.
Ever since hisgalos hakabalah, the tone of the vast majority of baalei machshava; the maharal, ramchal, gaon, chasidim, chid”a, and tons others has been a rejection of the philosophical approach to emunah of the rambam and instead the kabalistic approach of other rishonim including the ramban. At the same time, you have ancillary rabbis who were influenced by European enlightenment who all of the sudden found a leg to stand on with the rambam,. while lacking his allegiance to chazal and mesorah.
As stated above, the rambam was not anti-kabalah, he was simply not exposed to it; when he was, he expressed regret that he had not had it sooner – that’s a fact recorded by the abarbanel in the end of pirkei avos, perek 3. There is a famous testimony of the Migdal Oz as well, in which he found a letter of the rambam saying that he discovered kabalah and that he wishes to be more involved in it, and that the chachmei hakabalah are emes.
The rambam does not quote Aristotle for his shvil hazahav opinion, nor in any other context besides science and logic. He says clearly (deos, 1, 3-4) that “tzivu chachamim”, the chachamim commanded us to follow this path. Secular scholars on the rambam say that he got his middos teachings from Aristotle. The fiercest critics of the rambam, even the raavad on the mishnah torah, do not make this accusation. The Gaon, when arguing with the rambam’s denial of magic etc, says that here the rambam was drawn after philosophy. If his ethical approach was so greatly impacted and inspired by Aristotle (of which the Gaon knew a lot) he would have accused him of such. The rambam was not averse to quoting Aristotle when he sourced him, so why would he never – not once – quote him in an ethical or moral context?
As to chazal and their acceptance of three trials, see “torah chazal and science”, by rabbi moshe meiselman; he deals with that topic at length.