I don't really know how to explain this, but I mean something like "Oyasumi Punpun", where its really noticeable everything is good and pure at the beginning but then it develops into something darker, a mess...and its a really good development because you can see it and compare the end to the beginning, some kind of journey.
I usually read BL, but I'm open to any genre. Also, I don't care if its a manga, manhwa, manhua, or webtoon, or whatever.
I hope my explanation made sense, thank you in advance!!

That describes everything I've heard about the Digital Devil Story (Novel) series and it's spin-offs (With the exception the Shin Megami Tensei - Persona sub-series).

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Houseki no Kuni (calm as a water -> critical later)
Blue Flag (fluff -> heartbreaking)
Yume no Shizuku, Ougon no Torikago (harem stuff, tragic love affair -> political enemy. Hard to predict)
Vinland Saga (revenge madness -> find peace of mind)

I don't know if my recomm suits you, but I hope you enjoy it as much as I do.

Murasakiiro no Qualia
This Witch of Mine maybe
Tokyo Babylon (especially when you continue on with X as its sequel)

The beginning of Kitoh Mohiro's stuff usually has some of this (especially Bokurano and Narutaru), but things pretty quickly make a turn for the Sad and Depressing, so don't know how much this fits.

Also, Shoulder-a-Coffin Kuro is kind of the opposite trajectory, where it starts off kind of spooky but ends up in a really good place, but it's definitely a "story with notable development" and a literal (and metaphorical) journey.

There's also weird stuff like Game Club where things escalate kind of fast near the end, but you can also kind of see it coming from all the things that came before. I wouldn't call the beginning of the series "happy" by any stretch though.

Oh, and Higurashi series (starting with Higurashi no Naku Koro ni - Onikakushi Hen) is pretty notorious for this.