Considering Isekai is basically just fantasy with extra steps, take a look at Frieren if you haven't already. It's fantasy without the Isekai gimmick, following the story of an elf that outlives all her travelling companions, and retraces the steps of her journey with them to remember them. Very wholesome, slow paced and melancholic - even sad at times.

Ascendance of a Bookworm is another, following a library mega-nerd that isekais into a little sickly girl, and follows her story as she works towards creating the entire goddamn book industry all the way from creating paper from scratch.

Dr. Stone is potentially another example, not strictly iseka with the whole reincarnated gimmick, but "petrified for a few thousand years" and waking to a post post post apocalyptic stone age setting is basically the same anyway. Follows a science mega-nerd that starts recreating modern science from scratch.

I can second Ascendance of a Bookworm that has been mentioned. It's a very good series.

Escaflowne was mentioned too, which I found great back when I watched it, but it's been too long for me to remember. I want to rewatch it at some point. (Like I did with The Twelve Kingdoms which I found much less good today than back when I first watched it.)

I'll list a few more and add my rating assessment (ranking as exceptional, great, very good, good, decent, average, bad, …). I ended up going through the anidb isekai category, so I guess these are all I know of, and it's quite a lot of them considering it feels - as you describe it - like all or most isekai end up with lewd harem fantasies. As for the reason, I think it is primarily business people / production management producing for easy baits and the most generic middle audience - young males. Because of the success of isekais they produce more, and end up with the standard tropes of lewd, harem, and over powered, which very often ruins it. But as the following list shows, it's not always like that - even for an over-saturated filled category like isekai.

Handyman Saitou in Another World is another very good one that's not harem. Great comedy.

Grimgar: Ashes and Illusions is very different and very good.

The Magical Revolution of the Reincarnated Princess and the Genius Young Lady is very good until the ending, where it falls short and forces itself into something bad. The early and mid of the series is great though, with exceptional visuals and vibrancy.

I'm the Villainess, So I'm Taming the Final Boss is good. (Paired romance.)

In the Land of Leadale is good. Female protagonist.

Kuma Kuma Kuma Bear is simple but heartwarming, overall good within its simple formula. Female protagonist.

Life with an Ordinary Guy Who Reincarnated into a Total Fantasy Knockout is very good, great comedy with a gender bend/swap.

Now and Then, Here and There (2000) is great.

No Game No Life has a sibling pair as protagonists. (Prequel movie is great but not an isekai, the very good series is. Although it has its own share of "lewd service" IIRC.)

My Isekai Life: I Gained a Second Character Class and Became the Strongest Sage in the World! is only average, but a non-harem isekai as far as I remember and from what I can see skimming through.

Reincarnated as a Sword is good.

Saga of Tanya the Evil is good.

Saving 80,000 Gold in Another World for My Retirement is good. Female protagonist.

The Devil Is a Part-Timer! is very good.

The Great Jahy Will Not Be Defeated! is good.

The Twelve Kingdoms (2003) is decent.

Uncle from Another World is great.

Kagami no Kojou (2022, movie) is great.

If it's about the boy harem, there's those series with a female protagonist and reverse harem:

My Next Life as a Villainess: All Routes Lead to Doom! is good. (Otome-based.)

The Most Heretical Last Boss Queen: From Villainess to Savior is good. (Otome-based.)

Why Raeliana Ended Up at the Duke`s Mansion is good. May be reverse harem, or paired romance - I don't remember in particular. (Otome-based.)

Bofuri: I Don't Want to Get Hurt, So I'll Max Out My Defense. is not isekai transported, but videogame playing in world.

When broadening to fantasy, I rewatched Moribito - Guardian of the Spirit (2007) a little while ago, which has a strong female protagonist, and is exceptional. Definite recommendation.

Depending on how you look at it, this might be kinda the opposite of what you're asking for, but I thought I'd throw it out anyway in case you may still be interested: The Ideal Sponger Life is about a Japanese salaryman who gets isekai'd (willingly and intentionally, for a change) and marries the queen of a desert nation who needs a husband for political reasons but is reluctant to marry any of her statesmen (again, for political reasons).

The manga/novel (hasn't been animated just yet) mainly focuses on the political relationships between the nations of the isekai world, and the MC struggling to figure out how to reconcile his cultural differences while also being a decent diplomat for the sake of his nation and his wife.

Part of that is the fact that MC's marriage was initially purely political, but he and the queen grow to genuinely love each other. However, polygyny is the common practice in this new nation, especially among aristocrats, so MC is basically required to have a harem of wives, even though he very much doesn't want any other than the queen. This results in him having to find clever, politically acceptable ways to avoid advances from (shrewd, surprisingly well written) women who want to join his harem to garner power for their families.

In summary: It's a political fantasy story that is only technically a harem, and even then it's not ecchi/oblivious MC/blah, but an integral part of the political intrigue in the story. Don't know if that's still a deal breaker for you, but just give the first volume or two a shot. I went in with very low expectations and was blown away with how well the worldbuilding and characters were executed.

Ascendance of a bookworm - after you have watched it, come hang out in !aobanime@bookwormstory.social

How about ascendance of a bookworm?

No harem in sight only books and politics.

The og, escaflowne.

It might be overplayed, but Re:Zero does fit that bill. There is a romance, but only one, and it doesn't play off the ecchi comedy tropes. It still is based around an oblivious boy, but it's used as one of his major character flaws, and he has actual character growth.

It had a huge following when it was airing (still kinda does) to the point where it got annoying, but don't let that color your perspective of the show.

I haven’t seen all of it, but perhaps “I Don’t Want To Get Hurt So I Maxed Out My Defence”?

If playing in a video game and being stuck there counts as isekai, then Dr Stone getting teleportated to a future stone age world counts as an Isekai, and Dr. Stone is excellent.

Youjo senki is a good choice

The Faraway Paladin is my recommendation. It's so far off the normal isekai path that it's easy to forget it is one, and not a more traditional fantasy story.

Another older one would be Kyo Kara Maoh!, although it's a pseudo-reverse-harem in which the male protagonist ends up surrounded by a gang of bishounen (he ends up accidentally engaged to one of them, but even that's pretty mildly treated, and none of the others display jealousy or make passes).

Because it sells, but I'm also intrigued to know if anyone found something else.

I very highly recommend Saint's Magic Power is Omnipotent, I absolutely loved the first season and the second season is currently airing.

spirited away

Saihate no paladin is still what its supposed to be. A god damm good fantasy thats technicaly speaking an isekai.

Full Metal Alchemist: Brotherhood

Black Clover