There are people who view the Femme Fatale archetype as inherently sexist. At the same time when dealing with some especially older literature the Femme Fatales and other female villains are often the female characters that seem more real and relate-able (especially to female readers/viewers) since they alone are allowed to break traditional restrictions on what women can be. Add to that other reasons people often enjoy villains more, and they can be pretty cool.
With the Femme Fatale or The Vamp, I'm more concerned by the fact that that kind of villain never truly wins (in anything remotely mainstream). I know the bad guy winning is technically rare in general, but plenty of examples of it do exist. However every-time a Femme Fatale actually succeeds in seducing and ruining/destroying the "hero" of the story, it's always because he was a weak or horribly flawed character to begin with, in movies like Body Chemistry.
Often they think they're being feminist by doing it that way. (though the same scenario plays out in plenty of traditional works, like Samson, Samson was a morally weak hero. Of course Samson I believe was real so perhaps I shouldn't mention him when discussing fiction at all, but his story is told in a literary fashion). Sending the message that the man shouldn't really be allowed to blame the woman for his moral failings, and I understand that. Problem is plenty of female characters have been allowed to use being manipulated by a man as a valid excuse for their mistakes, and that too is thought of as a feminist rout to take.
And with that, every time a "Real Man" deals with a Femme Fatale he either resists, or if he has sex with her manages to turn the tables, it sends a message that women can't influence other people as well as men can.
The closest things I know of to exceptions to that are some of the Femme Fatales I really enjoy in French Pulp Fiction of the 19th Century, from Authors like Pal Feval and Ponson Du Terril. But even those are iffy.
Leaving that issue aside, I would also like to see more Heroic Femme Fatales.
There are lots of examples of a good female character briefly attempting to use her feminine wiles, but it's usually as nothing more then a momentary distraction (if it works at all) and still ultimately the Heroine just uses brute force to overcome her adversary (and recently even female villains using them turns out that way, like Mystique though out the X-Men films).
And again many may think they're being feminist doing it that way, thinking they're deconstructing or subverting the "problematic" Femme Fatale trope. But in fact the message it sends is that what society has long viewed as the masculine way to achieve a goal (brute force) is more valid.
But there is also the socially conservative reasoning, that a heroic woman could be smart enough to realize that's a weapon at her disposal but is not truly virtuous if she's actually any good at it.
A very notable exception to this is an old Pulp Character known as The Domino Lady, she was a very effective Heroic Femme Fatale, and I'm glad she's making a come back in New Pulp circles.
And as a Christian I'll point out that one of the Heroines of The Bible uses Sex to take out an Enemy of Israel. Jael in the Book of Judges. The poetic way it's described may make it difficult in English for some to notice, but in the Hebrew the sexual nature of that story is clear. She has sex with him when she "covers" him, if it meant covering him with a blanket he wouldn't become uncovered when she gets him something to drink. And similarly in the Apocrypha is Judith.
I also lament the fact that we aren't allowed to have Female Villians who are brains but not brawn anymore. Because people are afraid of sending the message that fighting is only for men. Yet plenty of male villains are still allowed to be super intelligent schemers who have others do their dirty work for them. It seems many attempts to correct mistakes of the past only result in what limits a female character being changed.
I also feel we Feminists should be less concerned about the truly evil Female villains. And more concerned when a male author seem to be unwilling to make a woman truly Evil. And that can happen whether or not the female villain in question uses Femme Fatale tactics. It is that kind of idealization of femininity that causes men to put women on Pedastools. Now I do love Redemption stories, I'm a Christian after all, but when a writer seems to consistently have female villains less evil then the males it's a frustrating pattern. It does not cause me to dislike the stories, but the pattern I feel should be noted. Now works like many Magical Girls shows where all villains male or female get redeemed in the end I'm all for as a universalist.
This is the only area where Lewis is better then Tolkien, he was more willing to have Female villains like the White Witch and the Green Witch. With Narnia anyway, in The Hideous Strength Mis Hardcastle, the only woman in NICE is also implied to be possibly not quite as evil as everyone else. But at least she's allowed to die without redeeming herself, my greater problem is that she is the only gay character Lewis ever wrote, and it's purely an example of her evilness rather then an attempted source of sympathy.
The most evil Feminine creatures Tolkien wrote were beings not even remotely human, like Ungoliant and the other Spiders descended from her. A lot of people feel Tolkien was very hard on the Queens of Numenor, but they were misguided if anything, not Evil.
Paul Feval, as much as I've praised his handling of female characters elsewhere, is in The Blackcoats possibly seemingly guilty of this. Marguerite, the only woman on the High Council of the Habits Noirs, is also the only one given any depth or sympathy (even The Colonel's love for his Granddaughter is described as being like the love one has for a pet). However she is also the only one given an origin story, in Heart of Steel, and in that early period is where all the humanity exists, once fully inducted into the High Council she seems as demonic as all the others. Plenty of lower level Blackcoats are sympathetic, like Ehcolaot and Similor, and also the Marchef, but the High Council members are depicted as pure archetypes of evil.
The Legend of Zelda has the same problem as Tolkien. Lots of completely inhuman monsters may have feminine names. But the only two major attempts at having a female main antagonist are Cia in Hyrule Warriors and Princess Hilda in A Link Between Worlds, one redeems herself in the end, and the other not exactly but she still clearly seems forgiven. Both were pawns of a greater evil to begin with. In the case of Cia she was split between her dark and light halves into two separate people, Cia and Lana, but the Dark Half is able to be sympathetic in the end while Lana shows no capacity for evilness at all, it makes no logical sense.
The Zelda franchise has had male villains play out somewhat similarly. But the greater evil is always Male (not always Ganon, some games do have no Ganon) and never Female.
Hilda was from the start a parallel Zelda so you may think "of course she was never really going to be Evil". But if we have a Dark Link why can't we have a Dark Zelda?
There is however a notorious fan-made Zelda game, an RPG called The Legend of Zelda: The Fallen Sage. Where the title character, Sulkaris, is female and is allowed to be as Evil as Ganon, no redemption in the end. In fact Sulkaris is the Morgoth of that version of the Zelda mythos.