Ha, I love this question. Artemis was definitely my favorite character at the beginning, and he's the one that really drew me into this series. I just like the idea of a villainous protagonist who slowly changes over time. (And I tend to like intellectual characters a lot of the time. XD)
However, over time, I feel like my focus shifted quite a bit over to Holly. Strangely enough, she wasn't a character I was particularly interested in at the beginning (I guess I just thought of her as the generic good-guy of the novel, and was interested in her mainly only as she related to Artemis. Plus she's probably my polar opposite in many ways, so I couldn't relate to her all that well). I think I first started getting interested in her as a character for herself at the beginning of TOD (that moment of vulnerability, after she saw Root die and thought Butler and Artemis were dead too, really grabbed me), and after I read TTP, I felt as though Colfer had intentionally made her real feelings on the matter with Artemis somewhat ambiguous, and I ended up delving into a kind of character study, to try to understand her background, her motivations, among other things about her as a person. Now I think Holly might be my favorite.
But, I guess I go back and forth. X3
“After all, absolutely no one can help but suspect a criminal, liar, and manipulator of committing crimes, lying, and manipulating. And of course, no one is more aware of that simple fact than Artemis Fowl.”
Opal sets into motion her most diabolical scheme yet, to frame Artemis and turn his closest friends against him. Only this time she has a new calculating partner who knows Artemis better than he knows himself. [An Artemis Fowl fanfiction, set after The Atlantic Complex.] https://www.fanfiction.net/s/8336552/1/Noble-Heart
...Shameless self-advertising, guys! C;
(And if you're really bored: http://axxonu.deviantart.com/gallery/28912232/Artemis-Fowl
AF fanart. ;J)