Two unpopular opinions about "Wicked":
(1) Without denying the importance of Glinda or the fact that the musical revolves around Elphaba's relationship with her, I prefer Fiyero as Elphaba's romantic partner.
(2) I don't think the message of the show can be summed up as "No one is all good or all bad." At least not in the sense the fans tend to use it, which (IMHO) is to gloss over certain characters' really bad actions with "Nobody's perfect, that's the point" and to paint false equivalence between Elphaba's few misdeeds and other characters' much, much worse ones.
And like granted, I've hated any bullies to lovers ship since I started getting into fandom, too, so... I'm definitely biased in that regard. I've never fucked with it, and I never will! And even if I didn't already hate bullies to lovers, I also definitely don't like how Glinda told Morrible and the Wizard how to capture Elphaba after Fiyero left with her- especially considering Elphaba was like, just as shocked that Fiyero chose her. Of course, I know it's not like, her fault fault that Nessa died, because she only said to start a rumor, not kill her, but still. It included the intent of them getting their hands on Elphaba. And of course Glinda isn't always the brightest in terms of planning, her strengths are much more in the social cog aspect ("form over content," "teach us history instead of always harping on the past," "did they have brains or knowledge," "its not about aptitude, its the way your viewed"), but she must have realized it wouldn't work out well to tell Elphaba's number one enemies how to get access to her
Also, there's just something so deeply appealing and sad to me about how Fiyero has always been adored for his looks, so he feeds into that, but not because he wants to. Because he's, imo, deeply convinced nobody in Oz could love him for his true personality. And so he acts up being careless and such, when in reality he's depressed as fuck and everything. And then there's Elphaba, the opposite. She's hated by all Oz for her looks, but knows if they just got to know her, people would love her. But, like Fiyero, nobody will look past her appearance. Until they meet each other. Fiyero loves Elphaba for, ironically, not loving him the second they met, since it's indicated she's the first person to ever do that ("I guess there's a first time for everything"), so of course he'd immediately be all heart eyes, because he knows that any feelings she has towards him will be genuine and not based on his appearance and persona.
And then, of course, he's transformed. He's, by his own standards, a freakish monster. And everything that was important to his persona is... gone. He lost his swagger a while ago, head-first into even worse depression while working under the Wizard and being engaged to Glinda, so that's gone. His looks are obviously gone. His ability to move all sexy like is gone- he can barely walk properly now. Even his status is gone, he's dead to all of Oz. He can't even go back to his family, and even if he did, they'd probably hate him. So, all in all, he's fully convinced that Elphaba will leave him. Even in his letter, he was all like, "I can only hope you'll still love me," or something. So like, his entire journey with Dorothy while figuring out how to escape Oz with Elphaba, he's just thinking she'll hate him and leave him like any other person would do. But she doesn't hate him, leave him, or think anything negative at all. And for me, nothing can compare to that.
Like obviously the show is about moral grayness, but Elphaba is pretty damn morally white. The only bad thing she's ever done was capture Dorothy- but let's be real now. The girl was coming after Elphaba, had her dead sisters and dead moms shoes, which may have very well been magic and valuable too! Obviously in the Broadway show, Nessa, iirc, shouts "my shoes, what are you doing to my shoes?" and obviously in the movie Nessa will fly instead, which, imo, will also be how Dorothy gets home, flying over the Impassable Desert like in the book. But in any case, of course Elphaba wouldn't want anyone else to have the magic shoes! That, and Elphaba was actively grieving what she thought was the death of the only person to sacrifice stuff for her (to that point). Given her line, "Fiyero, since I cannot succeed in saving you," it definitely points towards Elphaba believing Fiyero was dead as hell. Which is further demonstrated by how Elphaba wanted nothing to do with Glinda at Kiamo Ko until she got the letter as confirmation that Fiyero was alive. And nobody's mind is gonna be totally in check when death occurs, especially when the death happened because he gave up his life to save Elphaba's. Like of fucking course my homegirl was stressed out.
And, like you said, for people to put her on the same level as other characters is an insult for her. I mean, in what world is anything Elphaba doing equivalent to Morrible killing people and threatening the Monkey's families for obedience, the Wizard literally enacting a genocide and fueling propaganda??? Or even Glinda's actions- I mean, obviously Glinda's aren't half as bad as Morrible's and the Wizard's, but she's still not comparable to Elphaba. She bullied Elphaba for her skin, gave her almost nothing in the dorm, demanded Elphaba get her into Morrible's good graces for the bare minimum, mocked a professor for his physical incapability to say her name, led a song against Elphaba calling her disgustified, a terror, a tarter, intended to publicly humiliate Elphaba with the hat in act 1 (though she did change, obviously, but still). Then in act 2 she does nothing to help Elphaba- not because she was scared, but because she self admitted couldn't resist the pull of power and fame. Of course she feels terrible about it, but not terrible enough to change. And then, like I mentioned before, she told Morrible and the Wizard how to capture Elphaba as revenge for Fiyero leaving with her. Which is really upsetting, because, like, Elphaba didn't even know. She resigned her fate to never being with Fiyero. I get Glinda was pissed, and probably rightfully so (depends if Fiyero knew how she would react and was thus too scared to admit anything or not), but she didn't need to take it out on Elphaba, who was just as clueless as she was about Fiyero's true romantic feelings. And, of course, she does change for good and become, by all means, a wonderful person consumed by guilt. And I know and acknowledge she changed, but Elphaba never had to change! She was defending the Animals way before she and Glinda made friends. I mean, obviously the song 'For Good' is about them changing, but I'd also argue that the circumstances of Elphaba's half of the song do muddle the meaning a bit, since she knew she'd never see Glinda again. BUT ANYWAY
The only person of a similar moral level, though still not completely as pure, is maybe Fiyero. Of course, that's also because, well, almost all of Fiyero's motivations are unexplained. Like, did he lie to Glinda about his feelings because he's an emotional coward, or because he knew Glinda would react badly? Did Fiyero join the Guard and become Captain by spewing propaganda, or just by being a prince who was already dating Glinda? I mean, I'd ague the former seems unlikely since he tried to defend Elphaba, but I digress.
Anyway, the point is: nothing Elphaba does is even a quarter as bad as the other characters, and placing her a similar level to them is a disservice of her character and the sacrifices she's made to help those who need it. Like, imagine making yourself out to be a terrorist to help stop a genocide only for people to think you're of similar level to those causing the genocide and those doing nothing to stop it because they can't resist power. I'd be piiiiiiiiiiissed