One thing about Skyfall that bugged me

Also, I don't think anyone really "won" in the end.  Yeah, Silva ended up causing M's death, but given his reaction to her injury and his massive issues, I don't think he simply wanted her dead.  He wanted some sort of perverse reconciliation and closure, hence why he wanted her to end it for both of them.

I guess it works as an "everyone loses" ending, but it just seems like it left open an enormous possibility that was never realized.

Now, in terms of the actual plot, given how dramatic her death scene was I think it would have cheapened the entire thing if the film suddenly said "Aha, whoops! Looks like we made you all look like fools because here she is!". M had received a pretty brutal wound and had lost enough blood to merit her dying. Given the seriousness of the situation, she had no way to plan a faking of her death and Bond had no reason to be as emotionally torn up as he had been in the church when he held her as she died. If she was faking it, he wouldn't have been as upset, given the only person watching was the groundskeeper who wouldn't have been the least bit interested in revealing her survival.

Also, let's not forget how Bond made everyone believe he had died. He took a bullet to the chest and fell off a speeding train, falling completely out of everyone's sight. M died quite slowly whilst walking to a church, with both Bond and the farmer close by (And Silva, of course).

I don't think the lesson the characters took away at the end was connected to M's death, but rather the fact that the threats facing them were no longer from nations or other established groups, but could be anywhere, which is why they still needed spies.

Also, maybe I don't think the same way you do, but having her die, intentionally leaving clues to suggest she might've faked it, then turning around and saying "nope, just kidding, she's dead" doesn't add any weight to me.  If anything, it takes away weight.  If, for instance, they had established that she was going to try to fake her own death, and then something went wrong and she actually died, then that would've added weight.  I feel like if it was an intentional misdirection then it was poorly done.