One More Day: Yes, even though it was clearly contrived by the writers to get rid of the marriage (and therefore probably unintentional that it's there), Mephisto's "no soul" deal made sense-what happens every time he takes a hero's soul? A) Other heroes get it back, or B), Like with "pure" characters such as The Mighty Thor or the Silver Surfer (and maybe Spider-Man had that deal been made instead) he can't take the soul anyway because it's so pure it burns. He would have lost.
More Brilliance: He's semi-corrupted Spider-Man now. Spider-Man's soul is no longer pure, and Mephisto can get him next time...
I hate One More Day as much as the next Spidey fan but in Issue #500 Spider-Man has a vision of the future where he is wanted by the police and shot dead near Aunt May's grave. It's possible that Spider-Man remembers that and figures if Aunt May doesn't die, he'll never do whatever the hell he did to piss off the cops.
There was a moment of Brilliance for me regarding One More Day, of all things. Taking out the Deal with the Devil and 'magic retcon' thing, the Sadistic Choice presented is MJ (Spidey's future) or Aunt May (his past). The clincher is that it's his past, namely the death of Uncle Ben, that made him who he is. The whole 'power-responsibility' schtick pretty much mandates that Peter always be beholden to his origin...he'll always carry the guilt around of inadvertently letting Uncle Ben die. Aunt May pretty much exists to remind him of that. Is choosing to cling to the failures of his past healthy, or mentally sound? No. Is it consistent with the psychology of someone who was deeply traumatized by the previous untimely death of a family member? That's a dicier question.~Ingonyama
Although a bit of a meta example, while reading the 25th anniversary issue of Self-Parody series Spider-Ham, you'll notice the animal version of MJ is Mary Crane Watson, but one page later, among the heads showing characters in the Spider-Ham universe ("Larval Earth" or "Earth-8311", for those curious), you get to see former MJ counterpart Mary Jane Waterbuffalo. Then you remember One More Day and you remember the reason for such a change.
It gets better. MJ's looks since OMD have changed to be more overweight, in an attempt by Quesada to keep people from liking her.
Mephisto's Motive Rant contains a bit about how Peter's marriage was "blessed in the eyes of Him" or some other pseudo-religious wording, and it would be a sweet victory for Mephisto to successfully steal something from the One-Above-All. Which, y'know, makes sense: he's basically Satan. The problem? The One-Above-All is, according to supposed canon, not just an expy or Captain Ersatz of the Abrahamic God but actually the same literal person in a different universe. And Mephisto's plan to steal Spidey's marriage from him succeeds. He didn't just one-up the God of his universe; he one-upped the God of ours. Joe Quesada has created a comic that gives Christian/Jewish/vaguely-non-denominational-borderline-monotheistic children everywhere in Real Life the message "your God is fallible and can be beaten by a comic-book villain from another universe". And, despite living in a world where political correctness and cultural sensitivity are more common than ever so far he's more-or-less got away with that.
Likely because everyone's focus was on the bad choice of Peter and Mary Jane as well as the moral and logical failings of OMD and its fallout without even mentioning the insultingly anti-God undertone of the outcome. This might put us back into Fridge Brilliance territory, or simply be a little less horrible, because as most understandings have it, God allows humans to choose whether to accept Him and His blessings or the alternative consequences. It's less "your God is fallible", and more "anyone you look up to may choose Satan over God".
Of course, it could be considered a subversion since Mephisto's terrifying victory over God is....breaking up the marriage of two comic book characters. Temporarily. As diabolical schemes go that is....lame. Really lame. Especially since, according to [OMIT], it didn't even work. One would think the millions of souls he has ensnared into Hell or the countless lives he has ended or ruined would be more offensive to the Almighty...but nope. It's an annulment.
But maybe that's the key. Note that this is the only time Mephisto has shown Reality Warper level powers of this extent. Never before, never since thus far. Also, the main overall effect of all these changes is that years' worth of both power and character development have been taken away from Peter. Furthermore, Peter and MJ's unborn/future child was killed off by the deal as well; there go the lives she would've saved over the years in the future. Think about it. What if Mephisto's entire point was to weaken Spider-Man as a hero in order to set him up for a path more likely to lead to personal ruin if not to Gehenna itself, and what if letting the red devil have this marriage of theirs which was apparently blessed by God is what gave him that power?
Since OMIT basically says that Mary Jane scammed Mephisto, this creates a little Fridge Horror. Many comic fans can tell you that Mephisto's Berserk Button is getting cheated out of his deals. He has a tendency to take horrible, horrible revenge on someone who screwed him out of what he wanted. In other words, some horrible, painful event in Mary Jane's life was probably caused by Mephisto taking Revenge by Proxy on her.
For that matter, why didn't he make a deal with Doctor Doom at that point? For all that Doom is a villain, he can relate with desperately wanting to save someone you hold dear, given how he went out of his way to save his mom from Mephisto. In fact, Doom would have been the very first person to warn Peter against making any sort of deals with Mephisto, because they are never as clear cut as he presents them, while Doom at least always exposes clearly what he offers and what he expects in return. But no, Peter dismissed the idea because of Doom being 'evil'. As opposed to, you know, Mephisto the Boy Scout.
Doctor Doom also murdered his own girlfriend, made a magical costume out of her skin, and sold her soul to a trio of demons, demons who served Mephisto. In a story where he did not make clear what deals he was offering (twice - the girlfriend thought he was wanting to get back together with her; the Fantastic Four thought he was going to release their child from Hell if they surrendered.) And he doesn't especially like Spiderman, who foils his plans regularly and is good buddies of the man he hates most in the world. As you can guess, he probably shouldn't have bargained with Doom.
Actually Spiderman did try bargaining with him, but he and everybody else Dr. Strange let him visit said they couldn't do anything. This brings a whole new level of dumb. Spiderman goes to Dr. Strange, Reed Richards, Black Panther, Dr. Octopus, Hank Pyme, and Dr. Doom, and none of them can heal a simple bullet wound despite technology they have access to, or vast magical powers in Strange's case to the point where he at times has been criticized as a Deus ex Machina. As for Doom's dislike of Spidey, he probably would have made an effort to save Aunt May if Spidey had thougth to tell him, "Reed Richards admitted that he was incapable of doing this. So I came to you." Doom's done things like that in the past, just to prove he's better.
Actually, given that healing Aunt May would give Doom a chance to simultaneously show up both Reed Richards and Mephisto, who are Doom's #1 and #2 most hated entities in all of Marvel, you'd think he'd quite cheerfully break the space-time continuum trying.
He explicitly saved Reed's child to show up Reed (with the only part of the bargain being that he got to name the son so Reed could never forget it). If he's willing to do that for his hated enemy, I think he'd do the same for Spidey
Also, at what point in the creative process for the story was the idea "Time-traveling supervillain" not accepted? Seriously, if you want to do this kind of story fine, but for cryin' out loud, goofy ideas are better than mind-numbingly bad ones.
This option actually had a valid reason not to work. Time travel in Marvel Universe doesn't change history (unless it's a part of it) it simply creates an Alternate Universe. For same reason Peter couldn't simply go back in time and save aunt May. In cases when time travel does change the present (don't know why) it usually threatens to cause the end of the world and so has to be reversed ASAP. Or at least that's how it worked.
Actually, there are two people known to have invented a time travel method that avoids the 'many-worlds' problem and lets you actually change the main timeline, and ever since the Time Variance Authority was taken out of action again nothing stops them from using it (except each other, which is why they mostly don't). Of course, since these two people are (who didn't see this coming?) Reed Richards and Victor von Doom, we're right back to the original Headscratchers.
Elixir is a mutant who has brought people back from the literal edge of death before—he healed someone after their heart was torn out, an instantly fatal event, and they were fine and dandy afterwards. He couldn't heal Aunt May. Her injury? A sucking gunshot wound. So let us recap: a man with virtually omnipotent healing power, who can rewrite DNA at a distance and who brought another character back from an instantly fatal attack, an Omega Level mutant on par with Jean Grey in his particular field...was unable to repair the cellular damage (inconsequential damage by comparison) caused by a simple human gun. Mind you, even Angel, a much, much less powerful healer, was able to bring Jubilee back from the brink when she was crucified by the Church of Humanity. And compared to Elixir, Angel's healing power is basically a fresh bandaid. "Lol wut" doesn't even begin to cover it man.
On top of Elixir and Angel (and Lifeguard and Darwin and a few others) after the Decimation the X-Men put together an entire team of super scientists all of whose field of study is the human body. Additionally, Beast was able to quickly contact a dozen or so super villains for whom fixing a bullet wound would have been almost no effort (Sugarman, Dark Beast, Mojo, Spiral, Mr. Sinister, ect.).