ok probably gonna regret engaging with htdm morons but let's go through this anyway.
Adam: the brand over his eye, this helps us understand why he's so spiteful and obsessive, but it also plays narratively by highlighting how his thirst for revenge and power blind him to his own mistakes and have taken him down a dark path.
Cinder: losing her arm and her eye are also thematically appropriate, the more Cinder seeks out power and submits herself to Salem, the more of herself she loses. also, she's very transparently a villain protagonist rather tgan purely evil and mark my fucking words, WILL end up losing the Grimm on her body and turning against Salem.
Ironwood: all of you idiots' favorite. he's lost significant portions of his body including his leg, half his torso, and both arms due to his unwillingness to just fucking stop pushing for 5 seconds and think. he's so certain of his own path that he has traded his body for it. and he doesn't even realize he's gotten the short end of the stick. also not purely a villain.
Mercury: lost his legs as part of killing his abusive father, they highlight the way that the scars of abuse frequently remain indefinitely, but do not define him. Mercury is pretty transparently a package deal with Emerald and will almost certainly end up on the good team during the Vacuo arc
Neo: firstly muteness is fundamentally different from the other examples here, secondly Neo was very transparently not a full villain and was one of a very small number of people who get to literally be reborn so nice try.
you missed Tyrion, who loses his tail because he underestimates the students and gets so wrapped up in his bloodthirst he can't focus on self preservation. this also demonstrates some of Ruby's morality as a paragon, in a lot of shows a paragon would hesitate before harming another person so grievously, not Ruby Rose. she sees the path to ending the fight and she takes it.
you also missed both Maria, who's blind because of Tock's attack and had until she met RWBYJNROQ chosen to look away from the harm done by Salem; and Pietro, who just happens to be chairbound seemingly without any connection to character or plot threads.
so that's Adam and Tyrion in the pure villain slot.
Cinder and Ironwood in the cool motive still murder slot.
Mercury and Neo in the it's complicated slot.
and Yang, Maria, and Pietro in the good guys slot.
seems pretty balanced to me.