We've all been critical of Joe Q, Bendis, JMS, and the like (and I'm no less guilty, I admit), but the thing is about criticism is that sometimes critics ought to put up or shut up.
So, if you were running Marvel, how would you run things? Bear in mind that this is ideal, and doesn't necessarily reflect the realities of the comics industry-I suppose it's as much about your ideal MU as anything else.
As for the way I'd handle it...
1) Decentralized storytelling. Characters don't need to continually guest star in each others' titles. If the writer on Spider-Man wants to keep Peter in the Spider-Ghetto, focussing only on Peter Parker and his supporting cast, he's free to do so. If a writer doesn't want the Avengers ever dealing with the X-Men, fine. If the Hulk never crosses paths with Wolverine as long as the writer doesn't want it, great.
Bear in mind, of course, that this only applies to certain characters, most notably the ones with titles. Iron Man may never interact with the Black Panther, but they can both be struggling against A.I.M., for example. Many of the familiar traits of the Marvel Universe-things like Vibranium, SHIELD, Atlantis, gamma radiation, the Mindscape, etc., would all be freely available for use, which shows that, even though there isn't always a plethora of guest stars and crossovers, there's still a lot of common ground. Someone like the Kingpin or the Red Skull, since they're not the focus of an ongoing title, could just as easily be used by different writers without difficulty. Kingpin might have some intrigues going against Daredevil at the very same time he's manipulating Sleepwalker to do something else.
In a nutshell, it basically means to keep the guest appearances and mega-crossovers at a minimum, and let writers decide if they want their characters to team up, fight, or whatever. In Lorendiac's Superhero Writings, Continuity of Isolation would be important, although writers could just as easily have their characters team up or whatever if they agreed on it beforehand.
2) Hands-off editorial control: What this means, basically, is few if any editorial mandated mega-events. Storylines like Maxmimum Carnage and Civil War probably wouldn't happen much if at all, going for things that have a more limited impact, like Acts of Vengeance. Inferno wouldn't require that Spider-Man put his monthly thrashing of Green Goblin on hold just so he can fight demons, for example.
Editorial would only intervene if writers were doing things that would drastically alter the very concept or nature of the character, or if it was so grossly out of character that it all but amounts to self-destruction. I've made it pretty clear over at the spider-forums what I'd put the brakes on, so I won't repeat it here. Another example would be, for instance, turning Hank Pym into a wife-beater; that would never happen on my watch. Lorendiac identifies this as Continuity of Theme or Tone.
I freely admit I'd also put the kibosh on anything that seems too Women-in-Refrigerators.
3) Organic storytelling, both in individual books and as a whole: Something like Civil War would only occur if the line as a whole was in some sort of serious trouble, or if the whole thing was stagnant. Smaller-scale events can happen all the time, of course, but these should be things that only affect a specific title or series of titles, instead of affecting the whole universe, as House of M and Civil War have done.
Same thing for individual stories-let the characters develop more slowly and gradually, instead of injecting all these radical changes one after another. The Spider-Marriage was built up over a few years, and when it finally happened, it was a natural outcome. Jim Rhodes had been developed for years in the Iron Man series, and so when Tony Stark took a hiatus to deal with his alcoholism, it was only natural that Rhodey would fill in for him until he got his head together, and could otherwise pinch-hit in the armor when necessary, such as if Iron Man and Stark needed to be seen at the same time. Portal had been shown to be experienced with the Darkhawk armor and his relationship with Chris Powell had been developed from almost the beginning, so when Chris was indisposed, Charles Little Sky could step up to the plate.
Turning Peter Parker into a teacher would be a natural growth of his interest in science and his previous experience-he was a lecturer at ESU-and would offer a way to expand the supporting cast with his students. The Professor Hulk could be seen as a way to help Banner get a grip on his life and the multiple personalities of the Hulk. All these things work out great-unlike some things I'm sure we can all mention.
Well, that would be my ideal version of Marvel. What's yours?
I would have your three points (decentralization, hands off storytelling, organic storytelling) and Gamma's ideas of a continuity cop, and a return of thought balloons, etc. (if the author wants it).
However I will add this to the following.
1. Four "Imprints of Ghettoization": I took the term "Ghettoization" from a spiderman post where spidey mainly deals with spiderman characters, etc. I would divide marvel into four "imprints" each a ghetto of sorts but not an absolute one. (If someone wants to do a MU/Ultimate crossover they can). These Imprints are as follows:
MARVEL UNIVERSE: Marvel Universe is the main home of the X-men, Avengers, Spider-Man, Hulk, etc. It is based on heros who act heroic, fight villains, save the day, etc. It'd have a return of the sense of fun and the magic/sci-fi elements currently missing in the modern era.
MARVEL VIGILANCE: Marvel vigilance would have a darker theme and more of a gritty street level tone as the heros in it are grim and gritty anti heros and vigilantes. This would be the home of Wolverine (outside of the X-men), Punisher, Daredevil, Moon Knight, and Ghost Rider.
MARVEL COSMIC: this would be a home to sci-fi heavy explorer or cosmic types such as Silver Surfer.
MARVEL ULTIMATE: This will be a more serious, realistic, alternate universe closer to the real world where crossovers effect reality. Sort of a mix of the Ultimate Universe with the Quesada version of marvel. This Universe will existfor Bendis and Miller type writers as well as traditional writers who want a grimmer universe that can change on a large scale.
All of whichexist in the same universe except ultimate which is an alternate reality. Also the slight (though not absolute) focus on ghettoizing them will limit the needless wolverine and punisher crossovers (unlessan author wants one).
2. No More Writing For Trades: I personally dislike the toneand feel of comics written especially for trades and I have enjoyed comics less since that trend started so I will end it.
3. A Balance of Tones: At any one time marvel will at least make one heroic book, one serious/gritty book, and one humorous book, with enough variety to appeal to all tastes.
4. Continuity Cop Expanded Duties: not only will the editor watch for continuity, but also for lapses in characterization and deviations from organic storytelling as well.