If they left out everything you can disable, you'd have a lot of people who would be complaining its too hard.
Oh I know that's a market reality. But often these things aren't necessarily the problem (glowing objectives, hard coded rope arrow points, ect...) it's the degree to which they're done, or how they're done. (Obnoxiously bright, boringly and shallowly implemented.)
I mean if you want to be really cynical, allowing these things to be toggled off is a tactical move to eke a few more sales out of people that otherwise wouldn't have touched it. And in truth, that's sort of how I feel about turning off parts of games sometimes. A game fully featured is the game a dev envisioned, I like to think. When bits and pieces of it are sliced off to accommodate people's preferences or needs, it may make the game playable. But you're not really getting the full experience, for better or worse. It's a gray scale from disabling HUDs to turning off major gameplay elements. I don't think it's always a good thing when that's what a game has to end up doing it to please as many people as possible.
When it comes to touchstone gaming landmarks, it's probably inevitable. But every once in a while you do wish someone would just....knock it out of the park. Instead of what we're arriving at more often, which is games with compromised loyalties and visions. Options aren't bad, but when it's handled wrong (like most of the game is built around features that, when turned off, make little sense or are balanced poorly), they can be.
I guess it's hard to respect a developer's intent when they reboot a classic game and make modern changes to the formula, harder than just dismissing it as a required fad for AAA gaming.