You know why I can't read 616 Marvel Comics these days without getting a big headache? Because rather than acknlowedge that some writing is just crap, and fixing it by means of a miniseries, or revisiting an earlier comic in the same title years later (like they've done repeatedly in the DC Universe), They try to work everything in to one solid continuity. Thats why bringing Claremont back to the X-men was a bad idea, he is digging up all of the little aspects of continuity that had been dead and buried because they CONFUSED THE HELL OUT OF EVERYONE.
Because of this, the DC Universe is interconnected and far more mature than a Universe where the destruction of New York City by Xorneto goes unnoticed by both the Fantastic Four, and Spider-Man, not to mention all the hundreds of other characters living in NYC. House of M will be interconnect things for a while, but it won't be permanent, and will end up messing up the X-Men continuity even more. The first Secret War didn't bring things together, the second is only being noticed in Bendis titles, and the Infinite Gauntless, and War, and whatever, never had long-lasting effects.
I'd rather a fluid continuity that was refreshed so it stays sensical and enjoyable, than a solid continuity that acknowledges every little thing. Thats where bad stories come from.
That being said, this problem shouldn't exist. If Bendis knew what he was doing, he shouldn't have dealt with Iron Man's origins unless he was willing to do it all. I mean, if they thought that the UU would take off, they should have known not to mess with the backstories of characters who would potentially have their own titles. Now Card gets to write it, and I'm fine writing off the half-assed original story. Maybe Tony was just having a bad dream, and it wasn't a flashback at all. Maybe Tony has screwed with the press into thinking he came from an entirely different background. Who knows what they'll do. But even though I dispise Orson Scott Card as a person, he's putting effort into making an origin that makes more sense to the character he is in Ultimates, and it'll be MUCH better than what Bendis did.
I have a much bigger problem with the Latveria situation, because the situations in those issues have been mentioned in realtime books. Specifically the Black Widow's role.... *shrug*