A post and comments over at Not Brisker Yeshivish goes down the same road we have been over here a few times, but it does not hurt to do chazarah, so contribute to the discussion there. Just to recap a few basic points yet again:
1) Most people would not simply open a Yoreh De'ah and start deciding halacha based on which arguments of the Shach or Taz appeal to them, especially if they are aware that gedolei ha'achronim and poskim have weighed in on the issue. Multiple views on an issue is not a license to pick and choose freely among them. Same should hold true of hilchos deyos and hashkafos as well -- picking and choosing without guidance and without regard to precedent is a recipe for disaster. Given our own shortsightedness in all areas of life, personal preference or "what makes sense" is often a poor guide to what is true.
2) Asking, "Does holding X make a person an apikores?" is the wrong question to use to determine whether to espouse a certain belief. You can make a lot of mistakes before meeting the technical definition of an apikores. According to the Ra'avad you can believe G-d has a body and not be an apikores. Yet, that certainly does not mean one should aspire to or champion such a belief as an ideal!
3) The statement that certain views of Rishonim have become less acceptable over time is not a strange concept, but is an idea that we live with every time we open a Shulchan Aruch and follow one view to the exclusion of others. Asking, "Are you labelling the Rambam an apikores?" if you reject his philosophy makes as much sense as asking, "Are you labelling the Rambam a mechalel Shabbos?" if we happen to follow other views in a hilchos shabbos sugya.
Before one weighs whether the Rambam would really subscribe to all that is currently attributed to his philosophy, I think it pays to ask whether the Moreh Nevuchim has really left a lasting impression on Jewish thought, more than other thinkers who have lived since? If not, the question which begs itself is why (other than personal preference, which carries very little weight) one would suddenly look to the Rambam more than other views of Rishonim and Achronim to shape one's philosophy. Fortunately, my question was answered by Rav Soloveitchik in "The Halakhic Mind" p. 92:
"Judging Maimonides' undertaking retrospectively, one must admit that the master whose thought shaped Jewish ideology for centuries to come did not succeed in making his interpretations of the commandments prevalent in our world perspective... The reluctance on the part of the Jewish homo religiosus to accept Maimonidean rationalistic ideas is not ascribable to any agnostic tendencies, but to the incontrovertible fact that such explanations neither edify not inspire the religious consciousness. They are essentially, if not entirely, valueless for the religious interests we have most at heart."