But actually Spider-Man's reception, compared to that of the X-Men, was the first source of dissonance to my thirteen year old self. It's true that every issue of a Spider-Man comic reminds you how much it "sucks" to be Peter Parker, but there are few Spider fans anywhere who wouldn't gladly trade places with him.
In fact, Peter Parker is basically an idealized version of the typical comics fan. He's geeky and introspective, but handsome even before his transformation. And then he gets to become this physical powerhouse, while still keeping the quality of his mind (as opposed to, say, the Hulk).
I'm thinking of a comment to a recent post where someone talks about the idea of Spider-Man as a sex machine. But OF COURSE he's good in bed. He's superhumanly hot, strong, agile, intuitive (yes, I think Spider Sense warns you when you're about to do something wrong in bed). He's basically the perfect guy, and jokes at his expense about being emotionally stunted are really just things most adult comics readers can relate to, and secretly think of as better than the alternative.
I would trade my problems for Peter Parker's any day of the week. Except for when he's maybe getting his eyes eaten out or something. Spider-Man's problems are really just there to mitigate the degree to which the character is actually a great big jerk off fantasy. And for longer than I've been alive the Spider-Man titles have thrived on little moments that show you that, despite J. Jonah Jameson's efforts, there are people in the public who love and appreciate the guy. Including the hottest women around.
But the X-Men have it completely different. No, I wouldn't trade places with Scott Summers -- though I probably would have when I was thirteen. I'd rather be me than Hank McCoy, and countless others. If the mutants have to keep setting up island (or asteroid, or whatever) nations, why shouldn't Peter Parker, Carol Danvers, Jessica Drew, and rest have to join them there?
But I take your point that it's really just a problem of dozens of writers having slightly different visions of a shared universe -- and the X books have long existed in their own unofficial continuity anyway. Actually I think all of us are 80-90% on the same page. But the Champions Online open beta ended just a few hours ago, and this is what I'm doing instead.