In all seriousness, they could say they killed him, but I really doubt he'd stay that way for very long. If nothing else it would be a perfect setup for later revealing him as the leader of the Brotherhood (which seems ridiculous, but I've read worse things).
The Demon's Souls/Dark Souls games do this quite nicely.
I say that's debatable. If a story-driven game is well done then it can be memorable. For instance I really liked the stories of these series: Mass Effect, Dead Space, Force Unleashed, others. They're not perfect, but I thought they were well done and memorable.
I'd say that's also debatable. In my view we only remember the best 5% to 10% of games from 10+ years back, because all of the giant piles of crap we were exposed to have been blocked from our memories. The games right now seem worse because we're just more aware of all the terrible ones, and fortunately we'll forget them in time.
I generally agree with you, but there's still an age aspect to it. Kids growing up now are much more likely to swear by Fable and Uncharted, but are less likely to care about A Link to the Past. My first real game experiences were with the NES, and while I did play some Atari 2600 I don't really care about the "classics" of Pacman, Donkey Kong, Space Invaders, or Pong, even though gamers a few years older than me will point to them as the best games ever.
Here's what I disagree with:
The standards for game story/plot has evolved beyond what the original was, and the original only did what it did because of hardware limitations. If I had to guess I'd say that more recent games are what Miyamoto actually wanted to make. Demon's Souls isn't the greatest example because it too has tons of story/plot elements that you can find by talking to people and reading item descriptions, plus story events can also just occur in levels in the right conditions. This is different than, say, "Dodongo hates smoke". Why? And what's a Dodongo? And how do I make smoke? I can remember explicitly stating these questions, and if the game had answered them in any way it would have been better for it.
There's also the fact that the original DID have the lock/key dynamic you're referring to. Several sections of the map couldn't be accessed without the ladder or raft, including certain dungeons. In several cases a dungeon was only accessible because of the item acquired in the previous dungeon, and in the few cases where you could access one early you couldn't get very far because you didn't have the item that would allow you to acquire the current dungeon's item which was itself necessary to access that second half (and boss) of the dungeon. The fact that later games have tweaked this dynamic to be more restrictive is probably the only reason you've noticed it.
In short, the games aren't as different as you believe, and they've only evolved over time to match current trends in game design.