That whole subplot felt out of place in CW and could have been slid nicely into SM:H, but it's already out there and, perhaps from Marvel's perspective, there's no point in running over it again.
I would say that it felt quite in place in CW. Not for what it meant for Peter's backstory but because of how it resonated with Tony's. Ever since IM1, a recurring motivation for Tony doing what he does is guilt over the death and suffering he caused, either though negligence or inaction. That got amplified somewhat after Avengers & AoU because now he has a ticking clock in the back of his mind. He can't shake the knowledge something major is on the horizon and it's been driving him even harder ever since. I rather think it was quite a neat bit of symmetry for them to have found the common thread between those two characters.
I might agree that something like this in SMH may have helped a little in explaining, or at least reminding the audience of Peter's motivations, but I honestly don't think it's necessary.
Assume for a second that one is coming to this film utterly blind. Never saw the Rami films, any of the cartoons and only with the vague cultural sense of who and what Spider-Man is about. What would such a person see?
A boy living with his aunt, for starters. That alone tells volumes. One may not know the exact circumstances (it's not really relevant), but simple logic says this is a person who has lost at least two, but possibly three parental figures. His passing mention of "what Aunt May has been though" is enough to conclude his uncle hasn't been "gone" very long and their silence on the subject is deafening.
To my way of thinking, this is not the story of Peter agonising over his guilt regarding Uncle Ben, it's the story of him desperately trying to fill that hole in his life with a new surrogate father and role model.
Personally, I liked that they kept the Uncle Ben stuff out of sight, at least for now. Both because it's been done and done again fairly recently, and also because it's still rather fresh and raw and clearly neither Peter or May are dealing with it. Indeed, they're both quite deliberately *not* dealing with it.
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