This is the way I see it: Stories can be good even if they are short and simple, as long as they are well thought and written, some of the items in this list may be just that. There are some stellar stories too.
Summer with Mia - There is a second one being made, it doesn't have the most epic story ever but it is kind of bittersweet, I enjoyed. Don't be fooled by the NTR tag, it's an optional episode that doesn't add much, you can ignore it completely. 3D Incest VN.
Make love not Waagh! - Short story about a couple in a world where fantasy races exist, vanilla in the sense that it's a common couple's story but a nice and sweet game nonetheless. 2D VN.
Utawarerumono - Apparently they took out the ero content in this game but still(when they show you a picture of the sky with stars you are probably banging someone), I'm hooked on this game, it's long and you get to discover the world together with the main character, there are mysteries you want answers to and there are a lot of characters. Although I didn't finish it yet I would recommend you playing it. It's a 2D visual novel with tactical battles like fire emblem.
I highly recommend it.
Majikoi - A very long 2D visual novel, it's very comedic and everything happens in a way you don't really expect, while the game doesn't have the super serious grand anime epic story the characters interact with each other in a organic way and you can't help but enjoy their friendship and the situations they get themselves in. The routes with the girls are each unique. I won't say more, I
highly recommend it.
Hoshizora no Memoria - A nice game, there is a big mystery that you are trying to figure out during the game, it's long and there are multiple routes. 2D VN.
Venus Blood Frontier - It's a world domination game with actual gameplay but on top of the story you also have these events that flesh out the characters and how far they have been corrupted, it's a VN with gameplay.
Evenicle - A different story than what I'm used to, the way things work in the world are interesting and even the monsters act in unique ways. The game is mostly open world with visual novel elements and the battles are actually fun. It's one of my favorites and there is a second one coming!
I highly recommend it.
Sanguine Rose - It's not a long game or even a game with a lot of different endings but it's well made and it has absolutely stellar art, a satisfying story overall.
Wicked Choices - I recently started playing this, I don't really know how well it will develop but from what I have seen you have a lot of different outcomes and the story gets interesting. 3D VN.
I'm sorry if I put way too much anime in my list but it's just that a lot of good 3D games are in development and most of the completed ones just stick to the usual and don't introduce anything super out of the ordinary, you will probably find better stories in long japanese visual novels(not all are worth it though, some are cliche cringy). I hope it helps!
