If the whole idea of this world was Wanda giving everyone their greatest desires, how is it some of them don't get that? A good example is the Fantastic Four: Reed and Sue died in the space expedition instead of being empowered; Ben is little more than Doom's pet rock-gorilla; and Johnny is an underground mecha fighter (which is, by the way, something Tony Stark is doing for a living as well). Doom, on the other hand, did get what he wanted (known worldwide as a better scientist than Reed, adored by people all over the world and an unscarred face).
Because it isn't. "House of M" is the reality Wanda thought Magneto desired, the consequences of it, such as Uncle Ben not dying, are unrelated.
At first it seems strange and incredibly tragic that Professor Xavier is dead, and makes readers wonder whose perfect world it is that he is gone for good. But Magneto wouldn't have wanted Xavier dead, and nobody else, upon being "woken up" by Layla seems to think that Xavier being dead was their "perfect world". Why is this? Because in Charles Xavier's perfect world, he died a meaningful deaththat led to humans and mutants living side-by-side in peace.
In House of M, the authors introduce Layla Miller, a young girl who is able to make characters remember that they are in fact part of a Cosmic Retcon by Scarlet Witch. After the event, she disappears for a bit before reappearing in X-Factor, where it is eventually revealed that she has the power to bring things back to life, only without a soul. Now, if you'll pardon a bit of Wild Mass Guessing, here's where the brilliance kicks in: everyone in House of M was dead except for the Scarlet Witch, who had killed everyone. Layla brought the people back to life, and they lost their souls in the process. For example, Spider-Man sells his marriage (but not his soul) to Mephisto in One More Day; Cyclops starts X-Force, a black-ops team that goes against the peaceful co-existence that the X-Men have gone for in the past; Emma Frost uses a Deadly Game to select students who will have continued education following the Decimation; Hawkeye decides to just outright murder Norman Osborn after he becomes head of S.H.I.E.L.D. replacement H.A.M.M.E.R.; and Doctor Strange starts using darker magic. Whilst it doesn't apply to everyone (Luke Cage, Iron Fist & Ms. Marvel, for example), a number of the characters who had their memories restored by Layla have been subject to some sort of derailment since House of M.
Avengers Annual (2012) offered the possibility that the Marvel universe after House of M isn't actually (or ultimately) real, just reality as Wanda created it in her madness. This could be Fridge Horror or Fridge Brilliance, depending on your perspective — all the character derailment of the last few years is due to the characters not being their real selves, but the people as Wanda imagines them to be.
When mentioning the Decimation, people usually snark that over 90% of mutants lost their powers, yet somehow almost none of the big names (Cyclops, Wolverine, etc.) were affected. Obviously, this is because Marvel couldn't just spontaneously de-power some of their biggest names, but if you think about it, there might be an in-universe explanation. On some level, Wanda must be aware that some mutants would be miserable without their abilities - especially those she knows, and has interacted with. She removes the abilities of thousands of mutants she's never met, and herself and her family (presumably because she thinks Pietro would be better off and wants to punish her father), but when it comes to the X-Men? Subconsciously, despite her madness and misery, she can't go through with it, and the effect is sporadic at best.
Alternatively, Wanda started with the mutants furthest away from her, and since her power-nullification affected her, it couldn't affect the people around her first. She also started with a general focus, and either ran out of power or out of will to continue when she started affecting people she knew.
Another alternative: Wanda could not take the powers of those who were opposing her, on account that they were already fighting her and the resistance was too much for the all-encompassing sweep; she could also not touch those who had already died in the M-timeline, because they were no longer there for her to remove their powers.
Spider-Woman questions if it's not best to leave the effects of Wanda's reality warp in place. It was revealed several years later in Secret Invasion that Jessica Drew had been replaced by a Skrull impostor before she joined the New Avengers & when she regains her memories of the original timeline, she doesn't blurt out "Holy crap, the last thing I remember was the Skrulls kidnapping me!" - "Jessica Drew" in the House of M timeline is Veranke, whose greatest desire was for the the restoration of the Skrull Empire.
This one was intentional. Per Word of God, Secret Invasion had been being planned since at least the beginning of the New Avengers comic book. The authors intentionally left several Chekhov's Guns around, for the time when the reveal was made and the fandom had to begin the big guessing of who was or wasn't a Skrull.
This does lead to a massive dose of Fridge Logic if true though as why didn't she try and betray them knowing that her beloved empire was about to wiped from history once more? A bullet in Layla's head, the right word in the right ear as to what was being planned... certainly would have made far more sense than her proceeding to actively try and thwart her own interests by going off to fight Wanda with everyone else.