I like how pulpy Blanchett went with the character, but her potential as a villain is really undermined every step of the way. While she seems ruthless enough, her most villainous acts (the slaughter of the soldiers at Area 51 and of the tribesmen at Akator) are carried out off-screen by henchmen. It doesn't help that her threatening of Marion's life to make Indy cooperate is just used to kick off a comic tiff between the couple. If the characters treat it as a joke when the bad guys have guns trained on them, how seriously are we supposed to take them? Spalko doesn't really have the menace nor the hissable qualities you'd want in an Indy baddie. Donovan, a much less colorful villain, nevertheless has the moment where he shoots Henry Sr. and gives Indy's final task a clock and some weight. Spalko doesn't really have that moment. At no point does she prove to be a credible threat to any of the main characters.
I also remain puzzled by the decision to make Spalko maybe have psychic powers but then again maybe not? It's an ambiguity that doesn't feel intentional (there was apparently a deleted scene that showed her powers to be legit) and it's certainly not welcome, because it's another example of the movie undermining her as an intimidating foe. When Indy scoffs at her psychic stuff, we're never really given any reason to think he is wrong to. We can kind of ascertain that Spalko's inability to "read" Indy and the skull's refusal to "speak" to her (by contrast to the "pure-hearted" professors, I guess) are related, but it's yet another idea in the movie that isn't developed to the point where it means anything. Why does it matter that she can't read Indy's mind if we never see her read anyone's?
Finally, Spalko is denied the kind of memorably grotesque death that any archnemesis in an Indy movie should be able to depend on. Bloodlessly disintegrating into CGI powder is really weak soup given the tradition it's following. Blanchett showed up to play, and it was squandered by shoddy material.