#40
The endgame of the previous game in this series, a handheld game, where the series' protagonist emotionally fails to complete her mission, is briefly depicted again at the start of this game. As it turns out, failing to exterminate the young creature will actually save her life in the end.

Then you'll just go mad when we get to #28. XD

But hey at least I have it at two spots higher this year, was #42.

#42 Fire Emblem Fates / 3DS

Time to throw some games under the bus. I enjoyed FE: Awakening enough for the one playthrough I did, but honestly, Fates, the Conquest and Revelation routes specifically, were great, it does away with some of the bullshit from Awakening like the respawning enemies at the start of the enemy turn, fixes the broken and random pair up system and Conquest delivers on some of the best and most challenging map designs in the series. Birthright is alright, a bit better than Awakening but not by much. But the overall package was good enough for me to invest over 100 hours in it. Not the best in the series, but fantastic in the gameplay department.

Major props to the OST, my favorite in the series so far.

#41 Guardian Heroes / XBLA

Originally a Saturn game that was remastered for Xbox Live Arcade, Guardian Heroes, developed by one of my favorites, Treasure Inc. is a fun beat em up game with RPG elements like level ups between levels, also add the multiple choices you can make between stages to reach different levels and endings, makes for a very replayable adventure with a fun cast of characters and a godly soundtrack.

#40 is definitely correct

As for #41, let's just say that it doesn't necessarily have to refer to one of the main 15 Final Fantasy games.

It's worse.

Skyward Sword is still an honourable mention this year, like last year. I did replay it shorty before BotW came out though, mostly anyway. Still liked it, but not enough to creep it's way into the top 50.

Also, I have no idea on your #40, the only rhythm games I ever played were a couple of Guitar Heroes.

So... I'm guessing Final Fantasy Tactics?

This one seemingly was a bit harder, it took a while until John19 guessed it.

Can you see it? Right there in the screenshot is my first hint: Building model citizens. In the logo of the Lego City Police Department.

Well, you probably know Lego games. You have a bit of adventure, a bit of action and fights, some puzzles and a lot of humor. Nothing too difficult, but not always completely obvious either. It is the right mix for a relaxing yet entertaining game. So I do like Lego games, although differently. Some were in my opinion badly constructed, but that is another topic.

Of the ones I played (and as there is a flood of Lego games, I played only a few) i liked Lego City Undercover the most. Additional to the basic Lego formula which is working just fine in the game, you have an open world that you can roam of you don't want to follow the main story and it has a lot to discover and a lot to do. The one major critic I can direct at the game are the loading times.

In the game you follow Chase McCain, a policeman that comes back to Lego City after two years. His former boss is now mayor and tells him the criminal Rex Fury he caught back then has fled prison. So he looks for the main witness in the case back then and his love that had rejected him Natalia, as he suspects Rex Fury will go after her.

The gamepad is actually utilized well in the game, that might have led to the statement I put in hint 6. But this year saw the release of the game on PS4, Xbox One and Switch, so you can play it on a more modern platform than WiiU.

Wikipedia, MobyGames, OGDB, IGDB

You're getting warmer.

Hint 4: The humans are the antagonists in this game. They are overly controlled by rules, cleanliness, industrialization.

Hint 2: Monsters vs. Aliens!

Hint for game #38: A pirate and his moneky!