As a Brit Illiya is the only one I'd instinctively only prononce Ill-ee-ya. Elia I'd go more for eh-lee-ya, like the E in Emma, Emily or Ella, or even Ey-lee-ya like in some irish and welsh names you can find in the UK, so if you're going for a spelling where 99% of people are going to get it right, then I'd recommend Illiya.
But also I'm the person who named my MC Khayla (pronounced Rayla) because she's from Qatar and Kh is a rolled R sound in arabic, and also a character named Aide pronounced AY-DEE like Hermione... So I just assume people are going to pronounce their names wrong until maybe one day there's a screen adaptation (which is unlikely) or they get to the part about Aide's past where they learn that her name comes from the initials A-D. I don't mind people pronouncing their names wrong though, I don't think it hurts their experience reading my comic.