I wondered about the contrast between Hanako-arc Hanako and Lilly-arc Hanako too and what warwise says is probably correct. In her own arc Hisao's attention puts additional pressure on Hanako. This may seem contradictory because Hanako likes Hisao and it's suggested she has a slight crush on him in both arcs, but just because she likes Hisao doesn't mean she automatically welcomes his extended attention. Hanako's self-esteem is VERY low and when someone suddenly shows interest in her, it's not a stretch to assume that Hanako's process of thinking goes along the lines of: "he may like me now, but if he were to learn more about me and get to know the real me he'll quickly be put off by me". It's probable that over the course of her arc, Hanako switches back and forth between wanting Hisao to get to know her better and being afraid he'll be turned off once he learns more about her.
In Lilly's arc, Lilly functions as attention lightning rod, keeping Hisao at a distance that's close enough to make Hanako feel she's made another friend, but not close enough to fear he'll get to know her to a point he won't like what he learns. As a result, many of Hanako's deeper issues are simply never revealed in Lilly's arc and you're left with the impression that extreme shyness is the worst of Hanako's problems. The misanthropy that largely feeds her insecurities never comes up. However, as a result, it's also never addressed since Hanako distances herself from Lilly and Hisao a bit after the latter two start going out. So I disagree with the notion that Hanako is better off in Lilly's arc. When Lilly returns from her brief visit to Scotland in the Lilly arc, Hanako is still the same as she's always been except slightly more comfortable around Hisao. At that same point in time in Hanako's arc, Hanako has picked up a boyfriend for herself, has openly talked about stuff she's never even mentioned to Lilly (details of the house fire, her being bullied by her former friends in elementary school, her silent misgivings about her friendship with Lilly) AND has managed to trust another human being on a deeper level for the first time in probably a decade. Hanako tearing down that particular wall around herself and confronting demons she never has to face in Lilly's arc is a very significant breakthrough for her and she still has several more weeks left to go before she'd reach the point in time where Lilly's arc ends. In the end, the events in Hanako's arc were more painful for her than the events in Lilly's arc, but sometimes the process of healing is a painful one.
Didn't Lilly mention in H's arc that Hanako had actually come right out and said that she liked Hisao during evening tea?
Nope. That would have made things a lot easier if that had been the case. During Hisao's phone call with Lilly (which is the last time he talks to her during Hanako's arc), Lilly STARTS telling Hisao about Hanako's feelings, but stops herself before the beans are spilled. What you're remembering is probably the evening tea scene in Sisterhood which takes place after Hanako and Hisao became an item.