Correct, it's BotW.

Mnementh was first of course, but I'm not counting anyways.

All wrong unfortunately.

Gonna add a final batch of hints to see if we can't clean things up a bit.

12) Ended on a heart-felt note

Hint 2: I'm not referring to the ending of the game's story

Hint 3: The word heart is the key.

Hint 4: It's not Kingdom Hearts, but...

Hint 5: It's the latest entry in a series that releases once per console generation

8) This remake greatly expanded upon the final chapters of the original

Hint 2: You definitely know the original, but the remake is semi-obscure

Hint 3: It's a fan made remake, but the original developer gave it the greenlight and it's available on their platform

7) To me this is the most disturbing horror game I've played

Hint 2: And yet the extra content added in the expanded version was very heartfelt

Hint 3: The game itself only turns into a horror game at the halfway point

6) After venturing further and further underground over the course of the game, you fight the final boss up in the sky

Hint 2: Venturing underground is only a side-activity for most of the game, you'll mainly be venturing into people's minds

6. Nice. Anno 1602 is right!

Ok, let me try to catch up

Firstly, some honorable mentions:

#55 - Bravely Default

What I enjoyed the most about this game is the battle system, which adds some extra depth to the traditional turn-based battles with the bravely/default system. The job system featured in this game is pretty deep and super fun to play with. Overall, it's an enjoyable experience with some really likeable characters such as Ringabel and Edea, though the pacing completely collapses in the last few chapters, with a lot of repetition involved to get the proper ending.

#54 - Mario & Luigi: Bowser's Inside Story

I love this game's unconventional setting of Bowser's interior, and also how you get to play as Bowser himself. The turn-based gameplay in this game, which makes use of the synergy between Mario and Luigi to deal more damage, is just super fun; and the overworld puzzles, also based on the cooperation between the brothers, are very well made. The humor is pretty good too.

#53 - Dark Cloud 2

The town-building feature in this game is super deep and addicting, seeing your towns grow and getting more populated is really satisfying. I also really like the sidequests that you do to get people to go to your towns. The story has some really nice moving moments, and the music and art-style are top-notch.

#52 - Jak & Daxter: The Precursor Legacy

I love the open-ended levels in this game and all the secrets and challenges you can find in them, the game really does a great job at giving the sense of being in a grand adventure. Jak feels pretty good to control and the platforming and combat experience in this are overall pretty satisfying.

#51 - Bravely Second: End Layer

While very similar to the first game in many aspects, the jobs it adds and the extra QoL features make it an even more enjoyable experience, which leads to this game's turn-based system being one of my favorites overall. This game's story is much better paced than that of the first game (it has no annoying repetition), and I really enjoyed the interactions between the main characters.

Now, the actual Top 50:

#50 - Tales of Graces f

This game shines mainly thanks to its incredibly well designed and fluid battle system, which is complemented by addicting gameplay sub-systems such as leveling up Titles to get stronger, or synthesizing equipment via "dualizing".  I also really like the interactions between the characters in this game, especially through the Skits, but sadly the main plot is kind of a mess.

#49 - Tales of Symphonia

My first experience with the Tales of series, I really enjoyed this game's characters and their interactions and, while the story is not exactly the most original, it still is engaging enough, and has some really nice memorable events. Also, this game actually has some well designed dungeons with puzzles, something that is sorely missing in newer entries. The battle system feels pretty dated though.

#48 - Mario Kart 8 Deluxe

Going from MKWii and MK7 to this is mindblowing (I skipped the original Wii U version), and it's definitely the ultimate MK experience so far, I think my favorite thing about it is the 200cc mode, which gives an extra sense of speed that I really love, and sometimes makes it hard to return to slower modes. Of course, higher speeds mean you actually have to learn to use the brakes, so your driving abilities are more important than ever to get a good result. Also, thankfully this version has a proper Battle Mode.

#47 - Super Mario RPG: Legend of the Seven Stars

This game is such a charming grand adventure, with many memorable characters, great humor, and a story that doesn't follow some of the most obvious conventions of the Mario games. The battle system is relatively simple, but it adds some extra interactivity in the form of the "Action Commands", which allow to deal extra damage or to reduce the damage received when executed with the proper timing. 

#46 - Paper Mario

Another great Mario RPG, but this one has a peculiar art-style which plays with the idea that all the people in the game's world are made of paper. This game features some really charming characters, good humor, very well designed dungeons where you'll have to make use of your partners' abilities to solve puzzles, and an engaging battle system which expands on the idea of the Action Commands.

#45 - ICO

I think this game shines mainly thanks to the way it makes you feel actually attached to the character Yorda which, in combination with the mysterious and somewhat depressing atmosphere, helps to make the whole experience very emotionally impacting (dat ending). Another aspect of this game that I really like is how different areas of the palace are actually interconnected, which you start noticing as you advance through the game.

#17

Final Fantasy VI (SNES)

YoY: =

I never actually owned an SNES growing up, and although a few of my friends did, none of them had Final Fantasy VI, so I never actually got the chance to play it until I discovered they joy of emulation in the early 2000s. By that time I had already played through three or four other Final Fantasy games, and owned a PS2, video game graphics had advanced far beyond what the SNES was capable of, and yet, none of that diminished my enjoyment of the game itself. It had already started to dawn on me that graphics aren't really the thing that makes any video game great, and Final Fantasy VI is the game that in many ways crystallized that for good. They're a nice bonus, but graphical quality is far down in the list of things that matter when it comes to great games.

Final Fantasy VI is the first true masterpiece in the series, the game that gave us some of the most iconic characters and moments in video game history, one of the best video game soundtracks of all time, and the best SNES game ever made. Simply put, It's an amazing game, and features one of the best video game stories to this day.

Guessed by The_Liquid_Laser

In my list there area quite a few city building and management games. The "construction and management simulation" as Wikipedia nicely calls it. There's still some more to come even when we're at #9 right now. You can really subdivide these games in two categories; the pure city builder, that is exactly that, where you build a large city from a more zoomed out perspective 'zoning' entire areas at once, and the more strategic management variety where you have to create something more zoomed in and set up supply chains and keep people supplied with goods and specific buildings. 'SimCity 4' is the quintessential example of the first type.

As far as I know, this is still the game where you can make the biggest city, and the one where you can just make whatever you want in the easiest most intuitive way. Maybe 'Cities: Skylines', if you use the so-called 81-tile mod, but still that's only one map. SimCity 4 has a load of maps tied together in one large region. It's up to you if treat that as sort of neighbourhoods part of one giant city, or all their own municipalities in one country. I made a whole bunch of those 'countries' over the years. With big cities, a capital (imaginary, because there's no such function), and smaller towns. I'd even imagine a history for this country and model some of the towns towards it. I had all the time to do so, I played this game non-stop for a very long time. It's one of the contenders of my most played game ever, because  I really like city building and management games.

Time for the Top 5, the rest has already been guessed. I'll start with just #5.

#5: The whole secret of the game is blatantly told on a mural halfway through the game, but when you first play it, you don't exactly realise what it means until the end boss explains it.

Three games remain unguessed. Second hints for each.

#4:

• An age is slowly coming to a close once again.
• The sun god's fear caused them to stop the end once.

#3:

• 32 years after The Great War, the destroyers return.
• At the end of first game, in the final moments of The Great War, humankind was cut off from Earth when the jump gate to our solar system was destroyed. 

#2:

• The Moon That Never Sets.
• Every 108 years it glows red, heralding the birth of the Moon Child.

14. This game features an outfit for the main character that the main character from a previous game wore.

13. This game has one of the most violent final fights in a video game.

12. This game is one continous camera shot.

11. This game has the most playable characters from this series. The setting has many steampunk influences.

10. This game has multiple stages where characters can fight. The gameplay is very fast paced compared to it's successors.

8. Sonic Mania?
7. Doki Doki Literature Club?
6.  Psychonauts?