S.Q.L. does not pronounce well in English, since it does not fit the pattern of an English word.
If we spelled it out phonetically, it would be "escuel", and the stress would fall naturally on the second syllable, as in "esCUel" (natural), rather than the last syllable, "escuEL" (unnatural).
On the other hand, "sequel" is an English word, and the stress falls naturally on the first syllable, "SEquel".
In English, as in all languages, the tendency is to adjust words so they sound right and fit the pattern of the language. Thus, "Sequel".
Any acronym that is pronounceable as a word tends to go that way. For instance, do you say "P.I.N." or "pin"? "S.A.T. or "sat"?