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Not sure how to answer this, since you've answered it yourself.

Gene, I'll give this a go... As a fan, there are inevitably certain stories and characters you would love to work with if you could only get your hands on them. Something in an earlier story you read sparked something and the need to comment on it or give it a special spin or whatever you're burning to do... Likely isn't going to make for a good story or one that serves the best interests of the character in the long term. Fanfic is rife with stories of Kirk or Spock in terrible agony, dying, with a mind-meld as the only possible means to deliver relief from the suffering. Often such melds lead to sex. To some fans, this is Ev-Er-ything you could ever want from Star Trek! Two men, deep personal friends, sharing one another's minds, consoling one another through the worst, most unimaginable pain...

But it has nothing whatsoever to do with how a professional Star Trek script is written. It has nothing to do with the five-year mission, seeking out new life, or even the basic requirements of a three-act television script. It would also be the last story that could ever be done be the characters of Kirk and Spock as we know them because they would either be dead or lovers afterwards. "But that would be so great!" the fannish fans enthuse... Real story progression! Forward motion! And it would be great. For that one-one-hundred-thousandth of the audience. The appeal would be lost on everyone else and the actual dialogue, pacing, etc. would likely reek of amatuerism.

You don't have to love the characters to do a professionally written script about them. You just have to know them fairly well and be able to write professionally. One of the giant red-flag moments in recent comic book history for me was when Mark Waid joined a DC convention panel for a few minutes, announcing that he was going to write the next big Legion reboot (whereas he only edited the last two...) Questions from the audience flew fast and furiously, but he had somewhere else he had to be. Not to worry, he told the audience as he was leaving. "No one loves the Legion more than I do!"

And I knew the book was in trouble. Because LOVE isn't what makes the world go around. Not in professional circles anyway. And sure enough, the book was some nonsense about the Legion as a youth movement in a world of evil grown-ups, with all the "kids" of course being about two weeks from adulthood themselves. Characters were reduced to bad jokes. Colossal Boy wanted to be named "Micro-Lad" because all of the people on his world are big, y'see, and he had the special power to turn small, like the rest of us. See? Micro-Lad! Funny, right? Right? Yeah, not especially so... Not really. And really not a solid basis for the character to build on in the future, either.

But who cares about that, right? It's about love! Who knows how long he had that joke up his sleeve? Because he loves the Legion!

You can't really build a future on that kind of love. You have to have professionally written scripts that preserve the integrity of the product and the brand. You need imaginative, involving material that nevertheless leaves something for the next issue to build on.

That "first script you want to do as a fan" probably hasn't been written yet for a reason. You need to let go of that clingy, needy kind of fan-drama that results in epic pain or epic silliness for the characters and focus on good storytelling, absent your fannish inclinations to finally make the Yellow Peri a sales success or to finally marry off Vartox and Lana Lang for good. Those are weird little character fetishes. They're not stories.

Do not get me started on the Saturn Girl/ Proty marraige...

Today's writers may in fact not be traditional fanboys who have stories about these characters they've been dying to tell since they were thirteen, but the market today is completely built around an audience that is. The product nowadays therefore plays directly for that sweet spot with the characters in horrific pain with entire cities in rubble because Miracleman #15 was the god-damn-coolest-thing-any-modern-comic-book-reader-has ever-seen!

There is no protection for the characters anymore, no consideration for preserving any sort of basic premise for the future. Marvin gets eaten by Wonderdog and Bizarro punches the dead corpse of the Human Bomb until his "pretty lights go out." Forget the future. It can take care of itself. Right now, we've got stuff to do... (See also: Modern Energy Policy.) No one cares if we make Reed responsible for a nutty Thor clone who killed who-knows-how-many-people and that Reed did it all over some failed government policy. You know what? We don't need to save Reed from that. Three years from now, no one's going to care anyway! Other stuff will be happening! Why not do the fanboy thing? The fanboy thing sells like hotcakes to fanboys!  And really, the fanboys are the only ones left, so we may as well try to make them happy...

Controversy for controversy's sake sells. You know, if we did a story where we said Bruce was gay and the reason he didn't turn into the Hulk that time he was about to be raped at the Y was because secretly he was into it, we'd sell some books. Later, we just chalk it up to that Bereet lady making cheesy pornos now that he career's in the toilet. Yeah... 'Cause the Rampaging Hulk mag turned out to be all imaginary stuff anyway, something fanboys either already know or should know. And in the meantime we get some column inches out of the deal.

Sure, there'll be jokes about the name "Bruce" and the lavender pants, but those things are out there already... If we genuinely have reason to believe it will sell, it would be financial malfeasance and stockholder fraud NOT to do it...!!

Fanboy logic. Short emotional payoff, built on stupid events, with a firm reliance upon the lowest tricks of the medium to save our asses when the whole thing goes to hell, as Sins Past, Brand New Day, et al ad infinitum have... Let the characters fend for themselves. They're here for us, not the other way around. Stack the events, staggering them like Lego bricks so that when one storyline falls apart behind us, we're already onto the next one. As long as we keep moving, they'll never tag us out...

I don't hold with the idea that modern writers are all fanboys, but their output is exactly what would occur if fanboys ran the world, because fanboy-style entertainment is what is selling to the fanboys.

Editor: I need someone to write a history of our superheroes.

Pro: I'll do it! Imagine the scope, the grandeur!

Fan/Pro: I'll do it! At last we'll be able to show the origin of that obscure character who appeared in three panels of a cancelled series forty years ago!