Mayuri himself is subject to different interpretations. On one side, maybe he's a crazy Mad Scientist who is willing to do anything to further his research. On the other hand, he may be trying to atone for what he did in the past by helping Uryu now that he knows who he is. A lot of people take the middle road and say he just does whatever he wants while being a rude bastard to everyone around him because he simply likes doing it. And the Third choice: torture victim. For most of the time he's (supposedly?) been committing atrocities he and all potential witnesses were under the influence of somebody who could completely control their perceptions and who'd have had a strong interest in using, interrogating, and (to cover any tracks) breaking the mind of the current Chief of Research and Development. And that's not a short period of time.
Or from the reader's perspective, is Aizen an Ass Pull happy, faux-profound complexity addict in a universe that seems to conform to random plot twists; or is Aizen a smug jackass who, realizing that his power is hypnosis and he's already very powerful in his own right, largely improvises and then tries to psyche his opponents out with absurd rants and claiming things are the will of the Hougyoku.Or maybe it's just schizophrenia.
And what's the true nature of his relationship with Kira Izuru? Were they truly just captain and vice-captain, and Izuru's fragile self-esteem neurotic tendencies, and extreme loyalty coupled with Gin's mind games were enough to push him over the edge, or was there something more going on?
Head Captian Yamamoto: Wise, grandfatherly sage, or deranged, senile old douchebag who uses the letter of the law as an excuse for his dickery? More evidence to the latter in the most recent arc, the only times he's involved himself in the battle so far have been to seal off Aizen, Gin and Tosen from interfering, though when Wonderweiss' pet blew out the old man's inferno he did nothing to replace it and to one-shot Allon after the creature nearly killed four Vice-Captains. More recently in the manga he's still not intervening despite the fact Aizen had just decimated the combined Shinigami/Vizard ranks alone despite being confirmed as one of the few individuals who could probably take Aizen in a head-on fight.
There's even a lot of this for many of the Espada:
Coyote Starrk: Sympathetic but dangerous Anti-Villain who fell in with the wrong crowd, or a blameless Woobie driven by loneliness and the desire to protect his True Companions?
Tier Harribel: Cold Dark Action Girl loyal to Aizen, or Mama Bear motivated entirely by a desire to protect her fraccion?
Nelliel Tu Odelschwanck: Was she effectively babysitting Nnoitra to stick it to his chauvinist beliefs, or was it due to her feeling obligated to protect a comrade (even if he was a prick)?
Ulquiorra Cifer: Dangerous and ruthless Manipulative Bastard that looks down on emotions, or stoic Noble Demon that wants to understand them? Furthermore, does he have Lima Syndrome for Orihime or not? And were his interactions with Orihime a form of psychological torture, or genuine attempts at trying to understand her POV or making her understand his?
Nnoitra Gilga: Vile chauvinist lashing out at everyone due to his own inferiority complex, or a man gripped with a deep despair for himself and the world that causes him to see death in battle as his only escape? As for his feelings towards Nel; horribly expressed lust or utter hate? Did he hate her because he felt she was babysitting him out of pity, or was it because she correctly pointed out his Fatal Flaw?
Grimmjow Jaegerjaquez: Ax-CrazyBlood Knight that cares only about fighting and killing others for fun, or likable badass with a chance of helping the heroes?
What about Ichigo? Is he a man who truly cares about his friends and will stop at nothing to save them, or has his trauma of his mother's death affected him so much that his need to protect people comes from his own perceived inability to save his mom?
Or is he a truly honorable (as opposed to "honorable") and heroic Only Sane Man who is willing to buck the Soul Society to do what's right? A society seen to be horribly backward, unequal and archaic, hidebound to the point of reactionary, and unable to perceive the snakes in its own nest, when it's leadership isn't straight up Lawful Evil.
And was he born to be a pawn that both Aizen and Urahara hoped they could use in their convoluted plans?
Orihime: There's quite a debate among shippers on whether or not Orihime's unrequited love for Ichigo is innocent and sincere or borderline obsession. Unsurprisingly, the ones who follow the latter are rabid Ulquiorra/Orihime or Ichigo/Rukia fans.
Shunsui Kyoraku could, on the basis of what little we know of him up until the Starrk fight, arguably fit under either Obfuscating Stupidity or Crouching Moron Hidden Badass. Or both. He can both genuinely like being a womanizing drunk and still play mind-games with any poor sod unfortunate enough to meet him when he feels obliged to actually fight. The different aspects we see suggested (unlike Starrk, he gets no internal monologue) aren't mutually exclusive, and in a sense the 'unpredictability' is entirely what he claims to be about.
Yoruichi Shihoin, though the "alternate" part really only factors into her relationship vis-a-vis SoiFon, which, despite a good deal of Les Yay teasing from omakes and art both from the author and the anime creators, has not been properly fleshed out, leads to multiple interpretations by the fandom: is she cruelly playing fast and loose with Soi Fon's obvious feelings and leading her on for her own sense of fun, is she aware and simply does not wish to return the feelings but also does not want to burden Soi Fon with rejection, or does she love her but is merely torn between different obligations which cause her to feel she must keep Soi Fon at arm's length?
Interestingly enough, she goes from calling Toshiro "Shiro-chan" when he's still a young boy to "Hitsugaya-kun" (although almost never the "Captain", as he insists) after he gets his Shikai, with the implication that going from First-Name Basis to Last-Name Basis indicates that she sees him as mature. Does this mean that she's starting to see him as more of an equal (even if he's higher-ranked and more powerful than she is), or if she's going from seeing him as like a kid brother to a possible boyfriend?
Does Ryuuken have Uryuu's best interests at heart, wanting to keep him out of a thankless, dangerous lifestyle, and just have a lousy way of showing it? Is he an Abusive Parent? Is he perhaps both? For the Abusive Parent score, it does not help that he has said some egregiously contemptuous and uncaring things to Uryuu and has a history of attempting to police whom his son does and does not have contact with (in as a child Uryuu's grandfather, and as a teenager "Shinigami and their associates", which amounts to pretty much everyone Uryuu knows aside from Ryuuken himself), which in Real Life is a major red flag for abusive behavior. On the other hand, Ryuuken has helped Uryuu when he needed it most (restoring his powers and treating his injuries after Ginjo attacked him) and the events and revelations of the Final Arc have proven that Ryuuken was certainly telling the truth about how much danger his son is in. The "Breaded Eggs" position is more-or-less that Ryuuken did act out of love, and picked what he thought was the least-bad of a crappy set of options: retiring as a Quincy and keeping Uryuu out of the spirit world entirely...but Ryuuken also took dissuading Uryuu MUCH farther than he ever should have. The Despair Event Horizon might have had something to do with that.
On the subject of parents, there's Isshin Kurosaki. Is he a well-meaning man who did what he could to prepare Ichigo for the kind of life having spiritual powers would bring him, and who only held back on telling him about his past because he might not be ready to hear it? Or has him keeping so many secrets from Ichigo done nothing more than cause him undue pain, especially since Ichigo usually ends up hearing it from the villains instead? Does he treat his son more like a weapon than a person, encouraging him to put himself in harm's way and only getting involved in his struggles when he absolutely has to, and putting too much trust in Urahara's complex and morally dubious plans? There's also the question of whether his "training" Ichigo by randomly assaulting him is physical abuse, even if Ichigo mostly shrugs it off. Even a couple of the other characters (and Isshin himself) have said that his parenting skills kind of suck. In fact, at one point Isshin suggests that, of the pair of them, Ryuuken's actually the better father, because at least he's honest and consistent about what he wants for his son...as shitty as those expectations may be.
With the reveal that Retsu Unohana was the first Kenpachi (Yachiru Unohana), Unohana's personality after the reveal brings up discussions on her current self, and how much of her kindly, motherly personality was fake or genuine. Was it her just acting like a kindly person in order to not cause trouble due to her former status as one of the biggest criminals in Soul Societies history, or did she truly change overtime after realizing how horrible she had become, and her few flashes of intimidation just a degree of old habits still poking through? Her taking on the persona again against Kenpachi brings this up again for similar reasons. Was it her unleashing something she had been repressing, finally now having the chance to relive some degree of her past life without feelings shame? Was it her forcing herself to act like the same cold and ruthless killer for the sake of making Kenpachi stop holding back, no longer truly feeling the exact same she used to? The story leans heavily towards it being her suppressing her past nature and finally cutting loose, but there are some elements of her that do suggest she has softened in the years since, such as her relationship with Isane being shown as completely genuine on her part.
The detail that Royd Lloyd's powers allow him to copy the memories and personality of the person he does it to has sparked a bit of this, in regards to his reaction to Yamamoto's Bankai having the power to call upon the skeletons of those killed by it's flames. Was it simply Royd Lloyd briefly having an In-UniverseOut-of-Character Alert while pretending to be Yhwach, having not expected such a power? Is it possible that he was reacting like Yhwach would have, given his powers let him copy memories and personality? The latter suggests that, at one point, Yhwach may have cared for his soldiers more then he does at the present, but given how he acts in the present, it again is possible that Royd was so startled by it, that he momentarily broke character.
Furthering this interpretation, the anime includes a new flashback revealing that before the Lichtreich attacked Soul Society, Ichibei Hyousube arrived to propose a non-aggression treaty, upon which Yhwach gave a small Motive Rant about feeling the emotions of the people who died and thus empowered him, revealing his frustrations and anger at the separation of Life and Death via the Soul King. Given the timeline, it lends credence to the idea that Yhwach, while still certainly brutal based on Bazz-B and Haschwalth's recollections and Yamamoto's testimony, may have still had some morals and humanity buried within him 1000 years ago, only to now truly be The Unfettered with no shred of morality or emotion in his methods or end-game.
Yhwach's frankly bizarre sense of morality, such as his apparent confusion towards Ichigo being pissed at him for killing the latter's mother Masaki or viewing subordinates being sacrificed to empower others as honorable. Is he genuinely that messed up in the head, or is he only saying these to mess with people?
Lawful Evil.