Story is a tricky one. While I would agree with you that the *plots* are simplistic and repetitive, the depth comes in from seeing how all the little characters in the world are affected by what's going on and how they react to it.
For example in OoT Ganondorf takes over the castle, kidnaps Zelda, and Link rescues her. Ho hum, same old. BUT, the way it affects the lives of Malon, Talon and Ingo and the whole dramatic shift their lives go through is compelling and we feel for them. The loveable bumbling slacker Talon and his cute daughter make a sweet pair, meanwhile you've got the ungrateful Ingo in the background feeling unappreciated, and he takes over the ranch when Ganon comes into power, and Talon is forced to leave, and Malon sadly and sweetly takes care of the horses and sings her mother's song to them, and a depressed Talon sleeps the day away in Kakariko. Then Link returns and teaches Ingo a lesson and there is a heartwarming reunion between father and daughter as he comes back to the ranch.
Another example is LA where, yeah, Link collects the 8 doodads and tackles the end boss, but along the way he fosters a growing, believable relationship with Marin.
I also like the characters of Zill's family on Outset Island and how they interact with each other, and the reveal of the pig named Link's fate.
LttP has a related but separate focus, where the characters serve to introduce and flesh out the mythos, which is also nice.
So while the *plots* may be nothing special, the storytelling *is*, because we get the cumulative sense through all the little characters of a rich, living breathing world. So when I say story, I don't mean plot, I mean storytelling, which might better be described as world-building, but that leaves out the important part of character explorations.
Sense of wonder exploring ancient ruins. A lot of dungeons in games feel like levels, but when you can make a dungeon actually feel old, and give it a strong atmosphere and music track, when you make it feel authentic, that's special.
Lush, rich environments. Hyrule is a gorgeous place, and combining that with the beautiful music, creates a relaxing immersive atmosphere that really feels great. Those time where you actually get the sensation of exploring a forest or field, with wind in the trees, and the water rippling, and the cut grass flying. It's special. It's invogorating, like fresh air.
Messing about in Hyrule is really important. Having all these random fun little things you can do like smash pots in houses, play with Cuccos, hunt gold skulltulas, fun little side things to distract you make the game feel rich because you can do it now or later and prioritize things differently on later playthroughs and decide if you want to putter around or get right to saving the world.
Little gift box surprises. Finding chests and secrets throughout the game is a bunch of fun, little rewards and has a child-like appeal to it.
Fun, wit, and humor. Zelda has a special fun-loving charm to much of its dialogue and characters. It's hard not to just grin because of how light-hearted and whimsical things can be.