Valkyria Chronicles?

#4
This is a strange game; by the looks of it, when you're playing it I mean, it seems to be a prequel, but I don't think it really is. Then, it's name implies it's a sequel, which it's definitely not, and afterwards it actually came to be considered a part of the spin-off series it created instead of the series that's in it's name! What?

I didn't play the hints game because I really suck at making hints and guessing them...well, aside from that hint where the answer was so obviously Kingdom Hearts  but I'll still post my list here:

Firstly, some runners-up:

#55 Uncharted 2: Among Thieves

#54 God of War III

#53 Ratchet & Clank Future: Tools of Destruction

#52 Sonic Generations

#51 Pokémon Emerald

And now the top 50:

#50 Ratchet & Clank (2016) - I think this game has the best gameplay of all the Ratchet games I've played, though it's a shame that it doesn't have a battle arena.

#49 Kingdom Hearts 3D: Dream Drop Distance - I acknowledge that this game has lots of problems like flow motion being broken and the story being a convoluted mess, but I'm a sucker for Kingdom Hearts and had a lot of fun playing this game. The Fantasia-based world is so incredibly amazing.

 #48 Mario & Luigi: Bowser's Inside Story - I love the idea of entering Bowser's body and the combat is super fun. Game has some really nice puzzles and overall good level design. 

 #47 Bravely Default - I love this game's combat and job system  and I think Edea and Ringabel are awesome. Its visuals and music are amazing. It would have been waaaaay higher in my list if the last few chapters weren't soooooo repetitive.

#46 Dragon Quest IX: Sentinels of the Starry Skies - Great battle system and job system and some of the mini-stories in towns are really charming, though I wish the game had proper party members with a personality and all.

#45 Dark Cloud 2 - I really liked building towns and all the georama stuff, as well as the side-quests that you can do to get people for your towns. Visuals and music are top notch.

#44 Devil May Cry 3 -  Reeeeeally amazing combat (though I think I wasn't good enough to explore all its deepness) and I love Dante's personality (+ he's hot :P). Boss battles are so epic too and I love the game's atmosphere.

#43 Ratchet & Clank: Up your Arsenal - This game is so content-packed and the humor is great. The combat is, of course, super fun.

#42 Tales of Graces f - This game has one of my favorite combat systems and gameplay sub-systems in any J-RPG ever and its gameplay is almost the sole reason why it's in the top 50. I also really liked the interactions between the characters.

#41 Super Mario RPG: Legend of the Seven Stars - It leaves Mario's conventions behind with Bowser not being the main villain and is actually playable, and Peach is not a damsel in distress (well, at the start she is, but it doesn't last much). Game just feels like a grand adventure and I like its battle system (though I prefer Paper Mario's :P).

That is the one.

Same here, I have some interesting picks from others, while wanting to replay some of my older favorites.

More hints.  I will try to make this round more straight forward than some of my earlier ones.

#4 In North America, this spinoff game was released just a few months after the series' most successful entry.
Hint 2: The story of this game is about two childhood friends who took two very different paths as adults.
Hint 3: This is a turn based tactical RPG.
Hint 4: This is a PS1 game.
Hint 5: This game had two sequels.  Although this is a PS1 game, the sequels ended up on Nintendo handheld devices.
Hint 6: Set in the world of Ivalice.
Hint 7: This tactical RPG is a spinoff from the most successful JRPG series of all time.

#3 “Since man first walked upright, he has looked to the stars and wondered, ‘Are we alone in this cold corner of space? If something is out there, would it be friend…or foe?’ What would this Earth man think if he could see a desperate space ship, fleeing at a speed faster than imagination? What would he think if he saw the impact of powerfully potent neutronic missiles upon its fragile frame? What would he make of the strange pod that ejected from the ruined remains, just in time to avoid its mysterious inhabitant’s destruction? And would he gape in wonder at the dozen or so strange canisters that burst from its hold and fell towards the atmosphere of our guileless globe? What emotion would pass through his mind as he observed these selfsame containers as they passed through our atmosphere and fell upon the surface of an unsuspecting metropolis? So many questions and so few answers…until now dear viewers…until now….”

Hint 2: This is a real time tactical RPG.
Hint 3: This PC game pays homage to silver age comic books, especially those created by Stan Lee and Jack Kirby.
Hint 4: The developer of this game is actually more well known for a game about an underwater city dedicated to Objectivist philosophy. 
Hint 5: In this game you control up to 4 super heroes on each mission, and you can usually pick which 4 you want to take from a much larger roster.  The super heroes were created by the game developers and do not come from the comic books.
Hint 6: In this PC game you control a Force of super heroes, fighting to protect the Freedoms of the people of Earth from Lord Dominion and his forces.

#2  I want to give you the whole picture
Yeah, I'd love to tell you more
The girl Messiah was your lover 
or maybe the girl next door?
The first one died and she can't come back
Because she's like no other
The other went in and brought you back
Which will be your lover?

Hint 2:  This game comes from a well known series.  However the ROM for this entry is approximately 700 times larger than the ROM for the previous entry.
Hint 3:  This is the first time a game from this series appeared on a Sony console.
Hint 4:  Sephiroth


#1  My list so far is dominated by arcade action games and fantasy RPGs.  This is an NES game.
Hint 2:  This NES game set the gold standard.

Pokemon Sun/Moon?

Okami?

Both correct!

Shadow of the Colossus?

#4 Super Mario 3D World / Wii U

I actually don’t have a lot to say about this game, it has some of the best level design I have seen in a platformer, in any video game even, with new mechanics every level spicing up the game, perfect soundtrack, colorful visuals, some fun boss fights and filled with charm. It’s just a really excellent game in terms of design. What makes it special is that it’s a game that makes me smile and laugh just like a kid all over again while I play it; it brings me back to my childhood, something that very few games are able to achieve.