I'm writing a philosophy paper relying heavily on Aristotle and discussing several of his primary terms, including their etymologies. Therefore I say words like ἐντελέχεια and θεωρεῖν a lot. Since a fundamental premise of my essay is that we lack straightforward English equivalents for these words, and their etymologies give us important clues to their meanings, I have to leave them untranslated. But untranslated does not necessarily mean written out in an unfamiliar script---I could transliterate these words as entelekheia and theorein.
Other writers who share my views on translation go both ways on this. For instance Heidegger, in Basic Concepts of Aristotelian Philosophy, reproduces Greek script, while Christopher Long, in The Ethics of Ontology, transliterates. (Though obviously their audiences are very different.) My advisor has not expressed any preference on this matter.
Given this lack of deciding factors, what speaks for, and what speaks against, transliterating all the Greek words I use? Which audiences prefer one over the other? How would the decision to pursue publication (I will almost certainly not pursue this, but I am curious) change things?