You're right, but the 360 version did release this year, and it sold way more than expected,

I'll give you that. 

Ninokuni
Dragon Crown
Spelunky/Guacamelee

1Beyond Two Souls.
2Kingdom Hearts 1.5 HD remix
3Mario 3d world
*I think Ni no Kuni deserves to be listed too.

Ni No Kuni- Really came out of nowhere, at least to me.
Dragon's Crown- was expecting only 500k LT but so far it's at 800k and still selling.
Soul Sacrifice- Expected major flop outside of Japan but has actually sold nearly 400k WW at retail, it's actually the highest selling new IP on Vita.

3. Super Mario 3D World (having a 25% attach ratio? 1 million copies sold on a console with only about 4.5 million units sold? Should never underestimate Mario's power again)
2. Luigi's Mansion: Dark Moon (with over 3 million copies sold, it's a sleeper hit of 2013)
1. Fire Emblem: Awakening (first Fire Emblem game to reach 1 million units sold physically while the serie was about to be abandoned? Deserved that #1 spot)

Agree with Mario 3D World.  Selling great.  Can't wait to get it and play it.

The others I cannot comment on as I have not been following them.

I'm going to list a few more than 3 titles. Deal with it.

• Grand Theft Auto 5 (PS360) - We all knew that GTA5 would be big. But did we know exactly how big? About 1 in 8 PS360 games sold in 2013 were copies of GTA5. That's the type of numbers that you'd expect from a bundled game on a young platform, not for the second iteration of a series on a pair of mature systems.
• The Last of Us (PS3) - Yeah, I know that I should have seen this game being a big hit, what with it coming from Naughty Dog and whatnot. But consider how much this game has accomplished! Last year, the closest thing we had to a breakout new series/IP was Nintendo Land, with about 1.4 million copies sold. The top 44 skus of 2012 were all either pre-2012 titles or were iterations of existing series. The Last of Us is in the Top 10 despite some strong competition, and is definately the biggest new "core" series since L.A. Noire in 2011. Not bad for a new series so late in a console's life.
• Luigi's Mansion: Dark Moon (3DS) - The second game in a series that had a dedicated fanbase, but was largely seen as irrelevant until its sequel came out. The 4th best-selling 3DS game in a year that brought names like Pokemon, Monster Hunter, and Animal Crossing to the table. NSMB2 wasn't going to sell THAT many copies in 2013, but for Luigi to come well above it is notable IMO.
• Minecraft (360) - Just the Retail Version. Minecraft was always a huge success, but the fact that an already widely sold game did as well as it did as a late retail rerelease on a secondary platform is astounding to me. It is proof that even in a digital future, there will be a market for retail games.
• Just Dance 2014 (Wii) - Who'd have thought that the best-selling game on a Nintendo console in 2013 could possibly be a 3rd party Wii title? Even accounting for the popularity of the Just Dance series, the fact that it hasn't completely collapsed on its original platform is interesting, especially considering how quickly the Music boom busted. It gives hope that the dance genre has room to continue growing in 2014 on new platforms.
• Call of Duty: Ghosts (PS4) - Considering the PS4's strong reputation amongst gamers in the middle of the year, did many of us really think that the best-selling PS4 game would be a PS3 port? By a wide margin? Say what you will about how this bodes for the future of the industry, it shows that the CoD franchise has a promising future, even if it was overshadowed by GTA5 this year.
• Donkey Kong Country Returns 3D (3DS) - It's a port of a couple year old Wii game. How did this already break a million copies sold? Especially when the 3DS has no shortage of platforming games. I guess people responded well to quality platforming on the 3DS, even if it was only 30 FPS.
• New Super Luigi U (Wii U) - In a year generally dominated by disappointment for the Wii U, this game stood out. Even before the bundling began, it sold surprisingly well despite being essentially a traditional expansion pack. Already, it's outpaced games like Pikmin 3 and Lego City Undercover, which weren't exactly flops either.
• Fire Emblem: Awakening (3DS) - What can I say? This is a long-runner franchise that only just now caught on in the West. Possible reasons are many, ranging from the game's stellar quality, a hunger for great JRPG's in the months before Pokemon, and fan awareness reaching a critical point. Anyway, this is now by far the best-selling entry in the Fire Emblem franchise, and has guaranteed the series a place in Nintendo's library.

SS was definitely unexpected to sell Extremly well! I thought it would do as much as 180k-200k lifetime and many people as well (maybe up to 250k) and its at about 400k now! Definetly great sales for  Vita

No it didn't. It was 2012's Summer of Arcade