You're not supposed to think a villain is good,if that happens then the writer has failed in making him/her unlikable.You can be a fan of that villain but by all definitions they can't be "good" in any way.
I quite disagree with this despite you're using the right definitions or terms for them.
To me the antagonist or main villain is the one against the protagonist. That is all.
For all a story might seem focused on people who choose to be always hostile, and they succeed in killing the antagonist whose motivations are logical and realistic. A good antagonist is one who looks bad, but thinking deeply about it, uncovers the opposite, or of a small plot twist.
I find a weak villain who is one who just likes to kill for fun, has no future goals, and a very cliche villain in my eyes, not fully developed, that's how it is, why just rude to all, even your recruits, what if they turn against you, which doesn't happen because they all think he's overpowered.
I myself don't find Naruto(the character) a good guy, for his goals are achieve peace towards freedom, but freedom always leads to chaos, neither Madara is, because his ways are as close to enslaving, creating fake happiness, if a good lead there will, it should be with order, and that's not even enough.
I'd also add to that, showing the bad point in villains and good points in the protagonist and his ways, but it turns otherwise by thinking deeply or revealing the truth very after, is my cup of tea.
Sasuke could easily just tell her the issue and warns her, but it would not be good to his character as he's a person who think he could do anything alone.
Chaos's question wasn't about why didn't he just say, it was why do people like it. (this sentence is not a response to you but general)