Marvel's current crossover event, AXIS, involves various characters having their ethical orientation "inverted": heroes become villians and vice versa. A deceptively simple premise that has been used throughout the history of superhero comics—but rarely on this scale—it has potential for interesting stories (as well as culminating in "things will never be the same" changes to the status quo).
Ironically, however, it is precisely the aspect of Marvel's characters that makes them unique—their moral complexity and nuance—that confounds efforts to "flip" them from good to evil or from evil to good, resulting in strange adn confusing choices in storytelling and characterization.
There are very few characters in the Marvel Universe who are unambiguously good or evil: Captain America (that is, Steve Rogers) and the Red Skull, who are not among the inverted, are the two obvious exceptions. (There could be others too: for instance, I'd throw in Spider-Man, pure of heart but imperfect in execution, who interestingly was also not inverted.) The vast majority of the Marvel heroes and villains, however, are more complex, the heroes struggling against their more base natures and the villains striving to some degree to find redemption or achieve noble ends. But this complexity, a hallmark of Marvel Comics since the firm of Lee, Kirby, Ditko, and Associates dreamed them up in the 1960s, makes it diffiult to simply "flip" their moral characters. As a result, in AXIS we see a wildly inconsistent approach to inversions, especially regarding several heroes and one villain in particular.
Throughout this series and its tie-ins, I've been fascinated and frustrated by two characters in particular, Iron Man and Doctor Doom, whom I've long found to be very similar in their moral characters. Essentially utilitarian in their ethics, both pursue their personal visions of "the good" while believing that the ends justify the means. This leads Iron Man, for example, to take the controversial actions he took during Civil War in order to protect the superhero community, and leads Doom to try to take over the world, time and time again, because—as shown well in the miniseries Doomwar—he believes in his heart that only his rule can save humanity. Of course, both also have massive egos which serve to enable their extreme actions in pursuit of their singular visions, granting each the perception of entitlement, even the duty, to use their superior intelligence to save the world, damn the costs (as well as indulge personal vendettas and grudges along the way), and it is this arrogance which often foils their greatest ambitions (especially in Doom's case).
But after they are inverted during AXIS, these two similar characters are spun in completely opposite directions. Iron Man is portrayed as a mustache-twirling Snidely, teasing the citizens of San Francisco with an Extremis app that can make them "perfect" and then charging them $100 per day to maintain it. (This could be seen merely as leveraging an extremely attractive—and presumably legal—product for maximum revenue, but that sort of behavior often represents evil in popular fiction, and in any case is quite a departure from Tony's recent corporate altruism.) In other words, whatever restraints Tony Stark once felt on his pursuit of the good, for himself or for the world, have been removed. But this is not Tony "inverted"—this is Tony squared, Tony unleashed, his buffers removed, all second-guessing forgotten, resulting in even more of a caricature of himself than (according to some) in Civil War.
On the other hand, Doom has been all but neutered, now positively apoplectic about all the pain he caused his beloved citizens of Latveria, on whom he bestows democracy (by fiat, natch) before embarking on a program of making amends like a charter member of Villains Anonymous. The once proud and noble Doom simpers to Valeria Richards (daughter of Sue and Reed, currently living with Dad's greatest enemy in a delightful act of childhood defiance) about his need to right his past wrongs and also protect himself Latveria from an inverted Scarlet Witch who wants revenge for the events of Avengers Disassembled, House of M, and her wimple. (He had nothing to do with last one, but she could be understandably pissed about it all the same.) He even admits to Valeria—brace yourself, true believers—that Reed Richards has "always been right."
While Iron Man's "inversion" magnified his worse impulses, Doom's robbed him of his best. He either no longer seems to want to save humanity—a change that, in itself, hardly seems heroic—or he no longer feels he can do it and that the way he was doing it was incorrect—which is not an ethical change but an empirical one about methods. The thing that was evil about Doom was the steps he was willing to take to serve his goal of saving the world, but his nobility came from his sense of purpose and the moral lines he was not willing to cross (matters of honor such as truthfulness and keeping promises). Where he was once a fascinating man of extremes, now he's been reduced in both his ambition and his arrogance.
How interesting it would have been if, instead, Doom had been inverted into a traditional one-dimensional villain instead, using his brilliance to rob banks. Then, at least, the reader would have been led to ponder the true complexity of Doom's character and wonder if he was really a villain to begin with, and in what ways he was different from a hero like Iron Man. (At least they didn't make him an angry blogger.)
It seems that what the inversions did was not to flip the overall ethical orientation of the affected heroes—except in the most simplistic way possible, turning nuanced moral characters into one-dimensional caricatures—but merely flip the degree to which they perceived limits on their activity: for example, Iron Man sees fewer limits and Doom sees more. Apart from Tony and Vic, the Scarlet Witch indulges her desire for revenge against Doom; the all-new Captain America (Sam Wilson) still fights crime, but more like the Punisher than he did as the Falcon; and the X-Men become very pro-active against humanity (making Cyclops look like Gandhi). None of them has become a villain per se, but simply less traditionally heroic by virtue of crossing lines that once they refused to cross.
The main idea of AXIS is to flip heroes and villains along the "axis" of good and evil. But given the complexity granted to most of the Marvel characters by their creators, and maintained over the years out of dedication to that vision, there is no simple axis to be found. Most Marvel characters express their heroism or villainy in nuanced and multifaceted ways, so there are many axes along with they can be inverted. For example, they can be flipped in one aspect of them (such as what remained of Tony's restraints on his pursuit of goals), flipped along more than one of them (such as Doom's loss of ambition and arrogance), or reduced to a simple black-and-white caricature (such as the Scarlet Witch of Vengeance).
Of course, the "fuzzy" method of inversion in AXIS may have been part of the creators' plan—it did result from a magical spell, after all, and magic is known for its unpredictability. But I think some great story possibilities were missed by not considering what truly makes the various Marvel characters heroes or villains—or both.