I don't remember exactly where, but I remember reading that Colfer stated... "Artemis..." something something "I never knew he would be the series..." I don't remember. "He was just some bad guy Holly encountered..." something like that. So I'm guessing Artemis was a side character originally, but he stole the spotlight...I feel awful in doing this, but I agree with you. Today I was just thinking how in his interview Colfer said 'I might do a book about Holly' .
I kind of wish Holly was the main character, I don't even know why. can you imagine "Holly Short and the time paradox?" hahahaha. Wait, holly is still kind of a main character, the views in the books changes from Holly, artemis, and sometimes foaly, but mostly holly and artemis 50/50.
Artemis fowl is infinitely cooler name, though.