Bullseye!

Warcraft 3 is correct! Had it removed from my top 50 for awhile simply because I no longer can play the game like I used to. It is one of very few games that I list more based on how I remember it instead of of much I like it today. 

25: Secret of Mana?

Yes!

The first hint might not be totally true now that I think about it. When I played the game I always thought the mana beast was the same creature as the dragon-like one you can fly around with. But that might not be the case at all.

Next batch entering the top 20.

#20: This game's chilly opening is actually halfway through the story. Guessed by Pajderman - Uncharted 2: Among Thieves

#19: In the overal chronology of this series, this game is in the opposite timeline you'd expect it to be if you look at it. Guessed by UnderwaterFunktown - The Legend of Zelda: Twilight Princess

#18: It is obvious that the developers had the time of their lives when developing this game. Still, some of their ideas never made into the game. For example, an idea was that you could reload your weapons by unplugging and re-inserting the rumble-pak. Guessed by UnderwaterFunktown - GoldenEye 007

#17: This game ends with the raising of the Victory Banner on top of the enemy's government building, in reality one of the most iconic images ever.

#16: Even though the blue bartender in the cutscene isn't very helpful at first, when the protagonist shows his civilised weapon he's suddenly a bit more open about things.

28. This 2015/2016 JRPG is from a media franchise that used to rival Pokemon. It featured a simple story and more than enough monsters to collect like the old ps1 games. The developers of this game used to make the Wild Arms series, and then they worked on Shining games, and more recently they assisted with Valkyria Chronicles remastered and Valkyria Chronicles 4.

There is Pokemon and then there was ____mon.

23. A military tactical RPG released for the PS3. The main character is a tank commander of an elite squad for a small country.

22. "Everybody is born with a gift. The gods bestow us all with a job only we can do. It is our fate."

21. One of the first western foreigners comes to Japan, he finds demons.

20. "Don’t listen to Ondore’s lies!"

Uncharted 2?

I myself mostly only played the single-player (and custom maps when multiplayer at times), but my best friend used to play Warcraft III multiplayer pretty much all the time. When I came over and we'd play games, I played Rollercoaster Tycoon or something and he'd be playing Warcraft, very competitively. He was very good as well, and he couldn't stand not getting the first profile icon at 25 wins (I believe) with a 100% win ratio lol. Just had to be 25-0. He had thousands of accounts because of that lol.

Now though, he just never plays it anymore, at all. Reforged took it all away in one fell swoop.

Correct!

19) This is a Zelda game. I'm gonna guess Wind Waker

18) Hmm gonna guess GoldenEye

28) I figured it was a Digimon game but I don't know much about them. I think Cyber Sleuth was one, maybe that?

The last one sounds familiar but can't quite place it

Alright 5 more games

20) A subtle hint was dropped at a potential film inspired by this game

19) Skill trees shaped like icons

18) Arguably still the most ambitious entry in a series that has strived to outdo itself every time

17) Bolvar, Magni, Tyrande, Gelbin

16) Remade, reborn, re____