Without characters like Queen Chrysalis, there would not be much of a contrast of good vs evil, the only thing that prevents me from being scared of Queen Chrysalis is that she is not real. Chrysalis either tries to destroy or subjugate her victims, none of those outcomes are any good for Equestria and worlds beyond. A good episode, yes, but it is also a reminder that peace can only last as long as there are individuals willing to defend it. Equestria is a lovely world that I adore very much, but like every other world, it has its imperfections.
Yeah, Chrysalis took down Celestia in a duel, but if Chrysalis was too easily defeated it would not have been an interesting battle, if an enemy is a weak threat, you would not have much of a story to tell, no real stakes in the conflict, to make a battle interesting in a story requires this sense that the heroes could lose if they don't pay attention. What I liked about this was Celestia's bravery when the outcome looked grim, people can say what they want about Celestia, but there is something she is not, is selfish, because she was prepared to make the ultimate sacrifice to protect her subjects, being caught off guard before it got to this point, does not change this.
What gets me is how people blamed Princess Celestia for being angry with Twilight Sparkle initially for accusing Princess Cadance, when a shapeshifter was literally using identity theft to mislead both of them without either of their knowledge. People are all too ready to care about the result without looking at the cause and effect part of the situation, think about it, if a shapeshifter in real life existed, especially if they were smart enough to mask their identity from cameras, it would be incredibly difficult to detect them without DNA evidence, and I doubt such advanced forensic investigation existed in Equestria G4, all they could do is go by what they can directly observe, and it took some time before they could ascertain what was going on.