(I also thought from the title that this topic was about giving characters the appearance of 3D depth/volume in the artistic sense hahaha).
My approach is to try to avoid categorising character traits as "good" or "bad", but to think of them in a more neutral way. Like yes, Rekki is brave and the first to throw a punch, while Subo is conflict-averse, and in a lot of stories, that'd make Rekki just always the cool, heroic one, because western media always depicts being brave and "active" rather than "passive" as positive and heroic, but instead, I try to frame it more neutrally. Rekki is always rushing into everything because she's desperate to be valued and she attaches value to performing that heroic archetype. Subo is passive because he'd rather choose not to try than to try and end up failing. It's just how those two characters are, and it can both help them and cause issues.
If you think of some traits as "positive" and some as "negative" then your idea of character development becomes about stomping out flaws and effectively losing the qualities that makes that character unique and compelling, rather than striving to be a better version of somebody who possesses certain traits.
One of my characters who will be appearing soon is autistic, and too often media depicts autism either as a disability that simply makes the character a burden on other people, or as a negative character trait that needs to be overcome or eradicated to become a "normal" person who can enjoy parties and doesn't get anxious over details. But as an autistic person, I know all too well that I can't get rid of my autistic traits, they're pretty literally hardwired into my brain and I can only learn to cope with them in order to be effective and/or get good at pretending to be neurotypical to make NT people feel at ease. Jules similarly will never have her autism magically cured, but she might learn to get over some of her paranoia and trust issues, and to value herself more.
Basically, I think you should love all the traits your character has and try to understand how that affects their worldview, and have them living with those traits and how they can be good or bad depending on the situation rather than deciding that "being empathetic is always good" (It's actually not necessarily the case, it can actually cause a person to lose sight of broader issues, become biased or easily swayed by emotion and engage in enabling behaviour) or "being vain is always bad" (a person who loves themselves and always wants to look their best could still be a good and charitable person too- perhaps their desire for good optics makes them actually put a lot of effort into doing nice things for people who need it). Let the traits just be neutral and the drama in the interplay between characters flow out of that.