Prologue
Let me start by in no way defending all Manga and all of Anime, yes some of it is bad, but that problem affects every form of Entertainment, for every Godfather there exists an equally bad Movie on the other side of the Spectrum.
To fight that Stereotype i will not show you the most obscure forms of anime and ask you to just give it a chance, that is probably the main reason you never got into it in the first place. No i would like to show a few that might just make you say #notallanime
Yes i can see the surprise, most Manga fans are not exactly in line to become the next Federer/Messi/Lebron but there are many Sports Mangas and Animes that evoke that feeling to cheer on them.
For me personally that is Hinomaru Zumou, the Story of a Boy that wants to be the best at Sumo. What makes Manga stand out a lot from "real" sport is the fact that you get to know more about their Path, as if you are right next to him along the way, you see him at his lowest and at his peak. What took Hinomaru Zumou to the Top was the Typical Underdog Story, because the Protagonist is not blessed with the perfect Body, but that does not stop him from Trying.
Many Sports Mangas do have quite "over the top" effects to hype it up more, very similar to Wresting, to make it look almost inhuman. That might not be for everyone.
As a big Fan of Big Wars there are quite a lot of Good Mangas that often take many parts of History and of course make a few changes here and there to make the Story more interesting. A lot of them are quite grounded in reality but not 100% accurate.
The Story of two of the greatest military commanders in history: The Roman Publius Cornelius Scipio and the Carthaginian Hannibal. It starts with Hannibal as a Kid and Follows the path to Rome. Unlike the next one this is quite accurate and in a way a picture version of a history book.
Kingdom provides a fictionalized account of the Warring States period primarily through the experiences of the war orphan Xin and his comrades as he fights to become the greatest general under the heavens, and in doing so, unifying China for the first time in history.
While many parts of it are Fictional, the fact that it uses many Historical accurate People in some form makes it one of my favorite Stories to follow along.
A Ronin (Samurai without a Master) called Musashi wanders from province to province in search of great swordsmen to polish his skills, yet finds a deeper meaning to his path than simply killing. While the journey is a personal one, it features many Charakters from the Sengoku period of feudal Japan.
One of the few elements that did draw me to manga in the first place was the entire Grimdark subgenre that often is missing in Western Media (with a few exceptions like Warhammer) WARNING: If you are looking for a Happy Story, none of these are for you, many involve Death and much worse.
Grave of Fireflies displays a Story after World War 2 and the struggle of 2 siblings to stay alive.
Probably the number 1 on every "Dark" manga list on the internet, is Berserk, the Story of the Man that went trough Hell. It follows the life story of Guts, a young man with a Giant Sword. While it might not be the darkest manga that was ever made it has a very interesting long Story.
The story revolves around the oppression that took place in the Middle Ages Switzerland. The main source of fear for the cantons came from the feudal lords of Austria, the Habsburg. Wolfsmund is the unapologetic stories of those unfortunate enough to be tracked by Leopold or caught at Wolfsmund by Wolfram.
As many parts of the Middle Ages were brutal, so is this Manga as it does not shy away from Torture and other forms of Punishment.
Manga has never been shy to address social Issues or to simply show a path that a certain system could mean in the Future.
Inuyashiki is a Sci-fi Tale of 2 People, both Transform because of a Meteorite and grants them the Power of a Terminator. Showing a man that only wants to do good and one that only wants to do bad. Asking the audience the question of "what if you had powers".
The Anime Series (Not the Movie!) with 2 seasons asks a very simple question: what if there was a Computer that decided on your Crimes and acts as Judge, Jury and assistant Executioner at the same Time? It follows Akane Tsunemori, a new Enforcer that keeps asking questions about her Job.
In the Real World China's pointsystem is very close to the Show's Sybil System, as the question becomes, who exactly judges what is right or wrong.
The Story follows a Japanese Doctor and one of his former patients, who is revealed to be a psychopathic serial-killer. The Manga or the Anime are both equally good, as they are slightly older (1994 manga, 2002 anime) the quality might not be as high as some other shows, but the Story is one of those that you don't forget that quickly.
Afterword
Of course there are many more that could be added to the list, including some that go into full horror, apocalypse stories and many more. But i simply wanted to display a few manga and anime that go beyond the "cute girl doing stuff" and show that there are others, that may not get as hyped as those shows (cute girls sell in every industry), but that really make manga a very interesting form of Entertainment.