#1 is easy, but choosing the runner-up isn't.

1. Persona 4 Golden
2. Grand Theft Auto V

The Last of Us comes close. I haven't completed Pokemon Y yet, but it could end up taking the runner-up spot when I do.

Goty - Mario 3d world
Runner up GTAV

1st The Last of Us
2nd Tearaway
3rd Grand Theft Auto V

Persona was last year; just because you played it this year doesn't make it a 2013 game. 

My Top 5: 

1 - The LEgend of Zelda: A Link Between worlds
2 - Assassin's Creed IV: Black Flag
3 - Pokemon X/Y
4 - Guacamelee
5 - ??? (Waiting to play Super Mario 3D World, then I'll decide between it, The LAst of Us, and Bioshock Infinite)

1. The last of us.
2. Bioshock infinite.

Honorable mention: GTA V and Metro Last light.

The last of Us Number 1

Fire Emblem 3DS/GTAV Number 2

Ni no kuni Number 3

Amazon must have delivered my pre-order 4 months late then.

I wouldn't want it to take the 2012 top spot from Final Fantasy XIII-2 anyway.

Game of the Year: The Legend of Zelda A Link Between Worlds
Runner-up: Assassin's Creed 4 Black Flag

you must be in Europe then, because it released in Japan and North America in June and November 2012, Respectively.  

And FFXIII-2?  Top game of the year?  Ouch, must have been a terrible year for you. 

My GOTY: Fire Emblem Awakening
Runner Up: Pokemon X/Y

2nd Runner Up: The Last of Us
3rd Runner Up: Metal Gear Rising

It's a bit odd electing 2 3DS games, but Fire Emblem and Pokemon are pretty much the only reasons why I still buy Nintendo handhelds. Fire Emblem is one of my favorite franchises ever, and it's one of the best rated games for the 3DS and of 2013 overall. However it is a challenging game, and it's really something only for the hardcore. This it's my GOTY. Fire Emblem is just such a well made, and refined JRPG, it's challenging, gorgeous, and has an interesting plot, with the most unique and interesting characters.

Pokemon got second because it's also damn awesome. A new type, really good looking graphics, Mega evolutions....however most of the new Pokemon are still ugly, same with most Mega Mutations too. Unless Nintendo does something about the creativity of new Pokemon, this franchise will start to receed.

As for the rest, I think 2013 has just been a meh year. Sure IGN game The Last of Us and GTA V a 10/10, and in general these two games have had high meta-scores, but I think they are over-rated. The Last of Us is good, and Naughty Dogs ability to tell a story is excellent. I especially loved the quick time scenes, like the one with Joel....you know, because they made you feel like you were involved in a lot of the big events in the game, instead of just witnessing them in cinematic. Still though, the game was praised for being super realistic because you had limited ammo, but it's not. You kill way way too many people in this game still, strangling people shouldn't be 100% successful, so easy, and it should alert other AI because it's not silent. Plus why is there such a small ammo cap? I played on Hard, and at times I found myself maxing out ammo. Can I really only hold 9 arrows? 18 9mm bullets? This bugged me a lot on New Game +, especially at the start when you only have a pistol.

Still a good game, The Last of Us would be my 2nd runner up, but it's funny how I feel I have to defend my point. This game is way over-rated, Uncharted is a much better Naughty Dog franchise.

As for GTA V, it's just GTA IV, but bigger. I don't much care for playing as 3 different people, and I'm starting to hate how the games always take place in one of 3 or 4 American cities.....as for the rest? CoD, AC, and Batman look like more of the same, I can't stand annual releases, nothing on PSV interests me, and Pikmin 3 looks cool, but I still don't like playing as more then 1 character, it doesn't look anywhere nearly as cool as Pikmin 1 did. Super Mario 3D Worlds looks awesome too, I really want to get this game, and play it co-op, but I'm still 2 Galaxy's behind in the series, and the gameplay still looks like the same old 3D Mario we have seen in SM64 and 3DLand. What else released this year? Bioshock is meh, Pandora's Tower is meh, and Tales of Xillia is fun, but it's not that different from Vespria. As for Ni no Kuni....haven't played it, but it looks awesome.

However I would give Metal Gear Rising my 3rd runner up, that game is a blast.

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All said and done, those are my GOTY's. I can see why they probably won't get the award for GOTY though, they aren't "popular" enough, or have a large enough audience.