While clearly the men are the leading characters of the piece and Eliza is "supporting" them, she is the leading actress in that specific show. She had a longer arc than the other women in the show, and I believe she's more important to the plot on the whole. Sure, she doesn't carry the plot. It's also not Eliza or Phillipa's fault that Lin simply wrote Angelica to be more interesting (and/or Renee is more interesting). If anything it's one of the few detriments in the writing of the piece (I also kind of don't like that Angelica disappears, never to be heard from again except as the narrator of Quiet Uptown).
What makes you think Fiyero is the lead of Wicked? Was Norbert Leo Butz nominated for any awards in that category? (I know he wasn't nominated for the Tony that year)
"Contentment, it seems, simply happens. It appears accompanied by no bravos and no tears."