The Willa arc worked for me in large part because it finally gave the heroes a villain they had good reason to care deeply about, and because I found the period of time where I was trying to figure out what was up with Willa, how much of her behavior came from trauma/flawed humanity and how much from supernatural conspiracies, effective and entertaining.

But I would argue that the show presents Willa and Wynona as closer not because of their ages, but because Willa as eldest child picked up on real tension around Waverly's presence in the family, which we get definite hints about even before the revelation that she "isn't even an Earp." Willa's main role is to exacerbate the existing tensions between Wynonna (who never wanted to be heir but is stuck with the job & self-sabotages) & Waverly (who would love that job but can't have it, and tries too hard to prove herself), and that definitely doesn't go away afer Willa is revealed as a villain and killed. I think Willa helps us see where Wynonna's sense of isolation and Waverly's insecurity come from, but neither of those problems is effectively resolved, and both have actually worsened by the season 1 finale.

(Now if you want to argue that Willa ultimately rates a bit too high on the Evil Camp scale, cackling over arranging for the murder of the entire town and not retaining a strong enough connection to Wynonna, I might agree. But she has plenty of company in that regard.)