Because the game design "is" the game. The visuals can be improved to bring things up to modern standards, but the design is what we fell in love with. The changes are far from miniscule, that's an absurd comment. The first thing anyone used to say when MM was mentioned is "oh man, that save system". That memorable feature has been entirely removed / changed. Nothing miniscule about that. Nothing miniscule about changes to the bomber's notebook, which is the facilitator to the game's sidequests, when the entire meat of the game is said sidequests. This isn't an ordinary Zelda. It relied on atmosphere, 'negative' design decisions (time pressure, losing progress, an unbeatable boss) and sidequests more than any other to leave its impression on you. All of these things are being smoothed off by the changes, quite obviously and deliberately. If you like the changes, fine, but it's obvious why fans of the original wouldn't, and it's obvious that these changes aren't minor.
You didn't offend me, I'm just surprised someone on a videogame forum is surprised that others enjoy making their own fun in games. That's a massively common occurrence, Messing around with game systems, even just a little bit, is fun for most gamers. Freedom is more fun than restriction.
Pretty sure in all my years with the MM fans, I have rarely seen any of them mention the save system as the first thing that comes to mind. Honestly, the ones that mentioned it specifically were the ones that didn't like how it worked - so when you asked someone why they don't like or haven't played the game, they mentioned the save system. It was arguably the #1 barrier of entry into the game.
The bombers notebook was fine and dandy, but admittedly hard to understand. Sure, we can say we get it now, but personally I had to use a guide back in 2000 to understand exactly how that notebook works, which tells me it was a great idea with a flawed design. Maybe it;s a bit TOO helpful now, but it's not like you HAVE to use it. It was always optional in the original and is still optional to use now.
The atmosphere really still feels intact to me, because I didn't play the game for the save system or for the bomber's notebook, but for the experience of the world I am in. If I failed, I didn't feel "more into" the game because man, I have to redo everything starting at day one - in fact, I felt frustrated to the point I didn't want to play anymore and kept wondering why Nintendo would include save points that don't let me return to them. I did power through it, but the save system sucked back then and I still LOVED the game. As for wanting to be punished for failing - just don't use the owl statues then. You can close your 3DS for that "temporary save" and then pick up and play later, fail, and still restart your 3 days. Like, you can literally do that anytime you want. The closing of the 3DS replaces that entire initial save system with the same idea, just usable anytime.