I'm not a huge fan of the isekai genre, but that doesn't mean I hate it either; its ubiquity is what makes me wonder why people don't just make straight up fantasy anime.
Frieren for example would be terrible if Frieren was actually some random person from earth who got sent into her setting (or, as Frieren's whole thing is outliving her comrades, her purple haired protege was the isekai'd protagonist); I understand how the isekai nature of an anime can also affect the anime, for example a character who has modern world knowledge he applies in the setting, or modern world tech, but if he just becomes a part of it, and NOTHING from his real life has any impact on the setting....then what's the point?
Overlord for example (which I didn't enjoy to be honest; I googled if he ever faces a challenge and nope, entire series and he has zero things that can challenge him) would not have been affected if he was just some lich who woke up a thousand/hundred years later.
Konosuba benefits from the isekai genre in that the isekai elements keep being relevant throughout (Spoilers:
spoiler
for example that guy who chose to reincarnate into the world with a powerful sword that Kazuma stole, or Kazuma dying and Aqua's replacement reviving him repeatedly, or that the demon lords at some point realized all their most annoying hero enemies keep starting in this one town and so decide to attack it, or that ancient scientist who turns out to be have been an isekai'd hero who creates stuff inspired by stuff he was a fan of
Most isekai animes today just seem to be wish fulfillment harem animes, which are a problem on their own as well, but they're paired with being isekais too (if you're wondering why I didn't make a thread on wish fulfillment harem animes, it's cause by and large I avoid them like the plague).
There are some interesting POST isekai stories that I found fascinating, stories where the characters came back from the isekai world and had their powers with them; in one case some of the heroes become devastatingly powerful villains who destroy entire cities, in another case it's a comedy about some guy who comes back and....could have been funnier without the ecchi/SA nonsense happening throughout.
Animes like SAO (which I didn't find interesting beyond the first story) make the other world an entirely false world and never let you forget the characters are real people who can actually die in the real world (sort of an anti-isekai genre).
In general, if they're not going to benefit from being isekai....then just make them normal fantasy. So many good fantasy animes out there that would have been hurt by making the protagonist just an isekai'd character.
I'm gonna attempt to make a list of isekais that are actually good (or at least slightly better that average for the genre).
Gyaru Maid to Akuyaku Reijou ~Ojou-sama no Happy End shika Katan!~
An isekaied gyaru become a "Villainess"'s maid. Gayness happens.
It's very short for the genre's standard (~15 chapters). The relationship between the main characters is cute.
Dahlia in Bloom: Crafting a Fresh Start with Magical Tools
Girl gets isekai'd, becomes a magic engineer.
This one is not very action oriented as the main character is too focused on making all kind of magic contraptions to go adventuring, instead the story focuses more on the MC as a person. The difficulties and obstacles she has to face to achieve her dream, and even some personal drama she has to go through.
So I'm a spider, so what?
Girl get isekai'd as a smol spider in the most dangerous monster filled underground labyrinth in the world, does her best to survive.
The final boss of the "reincarnated as a monster" sub-genre of isekai. The MC is funny, likable, relatable often, and has a pretty unique personality. She faces constant challenges as she grows stronger.
Sasaki and Peeps: That Time I Got Dragged into a Psychic Battle in Modern Times While Trying to Enjoy a Relaxing Life in Another World ~Looks Like Magical Girls Are On Deck~
Middle-aged guy buys a bird pet that turns out to be a mysterious mage from an other world. They both become friends and start traveling regularly between the two worlds and the MC starts learning magic from the bird/mage. They both end up tangled up with the nobility in the fantasy world and a secret government agency that recruit peoples with psychic powers in the MC's world.
This one is wild as the previous synopsis might indicate. It's pretty fun with how random the manga is yet still manages to take itself seriously when it needs to.
There are a few others I know but I can't be bothered to find them right now.