It means "No." By the very mention of wiki you should have realized thematic naming applies to the character; thematic naming dictates a set name for the mythological ruler of the wind. You don't change that. You can only change the theme you base the name on, not the name itself. As such, he's Helios in Rockman, Aeolus in MegaMan. The theme changed because they felt it more appropiate for the Wind MegaMan to be named after the god of winds instead of the god of the sun.
Beyond that, you seem to be fairly against the use of AE with any other vowel... AE is a common combination of vowels in latin that make a specific sound (Caesar, Aeolus). That specific sound is often abbreviated into a vowel of its own: Æ æ (Cæsar, Æolus). As you complain about the combination of ÆO, despite it being no more complicated than AO or EO, you only show your lack of familairity with the latin language and even that of English (Archaeology, Archæology).