Any manga recs for a yaoi or shounen ai with a really good story, where you feel emotionally invested in the story, I don't want it to be all about the smut, also I would like the head over heels seme to be pursuing the uke- a good example of what I am looking for is Yatteraneeze! Thanks-

I'll try the classics, just in case you haven't read them...

Yellow

Totally Captivated

The Finder Serires

Hope it helps =3

When life gives you lemons, you...make a loooot of yaoi! >3

Moved to Yaoi/Yuri~

There's already topics like this if you look around, such as Best Yaoi

*EDIT: blah. edited. It's because I didn't read OP's post thoroughly. :\ *

Love Mode - This one is pretty good. It's 11 volumes. It revolves around two couples. You'll grow to love the characters and their unique personalities. The art style is pretty old, but I can't deny that they still look pretty sexy. 🤣

The Tyrant Who Fall In Love - Maybe you've read this already, and I'm sure this one is quite popular.. it's popular for a reason: it's quite good, cute, funny. We've got one of the most stubborn characters in here. ( Takanaga Hinako's other works are great as well. )

Totally Captivated - it's cute. (was the seme totally pursuing the other guy in this series? I forgot.)

Kyuuso wa Cheese no Yume wo Miru
and its sequel

Seven Days is pretty sweet. Very warm fuzzy-ish.

I totally agree with totally captivated and all othe mangas that were named. Some other good ones are:
Komatta Toki ni wa Hoshi ni Kike! really nice shounen ai but nothing much happens , it's a really awesom comedy
Café Latte Rhapsody sweet story
Dear. Gentle Papa
Jazz
La Esperanca shounen ai
Kusatta Kyoushi no Houteishiki

takes a long long time till something happens

My Precious shounen ai
Rules
Running on Empty really enjoyable
Ouchou Haru no Yoi no Romance

there are a lot more I really liked but I think that's enough ^^

sakura gari

Let Dai - Quite possibly the best and most realistic shonen ai I have ever read.
Tokyo babylon - Clamp's best work ever. Once you get used to the art it's fantastic.
Fake - Lots of focus between the characters.
Shiiku Gakari Rika - WARNING: Very disturbing! Graphic and realistic sexual, mental and physical abuse. Horror.
A Night of a Thousand Dreams - Beautifull art and characterization.
Zankoku na Kami ga Shihaisuru - Winner of the first Osamu Tezuka Cultural Prize's Award for Excellence. Contains graphic abuse.

As for authors; just about everything by YAMADA Yugiand YONEDA Kou