Normally I'm more interested in the plot and what the characters do than empathising with them, but when a character strikes me as being particularly me-ish, it really catches my interest, because that doesn't happen often.
The interplay between Trevor Goodchild and Aeon Flux was a pretty interesting exploration of my internal conflicts, but I s'pose the point of the show was examining them because there's something of Trevor and Aeon in all of us. Me, more of Trevor, but just as captivated by life's Aeons.
Mm, other characters that struck a chord include Huey Freeman (the way he's defined by a frustrated, long-suffering but still intense idealism), Olivier Mira Armstrong (represents the kind of strength and confidence I want to have), Rei Hino/Sailor Mars (her critical nature, perfectionism and "vitriolic best buds" relationship with Usagi are very me), and Jane Lane (who's detached and snarky like Daria, but more open to intimacy and less naturally sure of herself).
Yeah, I tend to identify more with cartoon characters than those in books, live action TV or movies. Don't know what's up with that. I think they're easier to project on.