I know e3 didn't meet expectations, not even close. But still, I am still excited for at least SOME of the things they showed off. These are my top 3.

3.) Mario Maker - Even though we knew it was coming, I am still hyped just to see more gameplay of it.

2.) Xenoblade Chronicles X - Once again, we all knew it was coming, and the trailer is basically the same thing as last time, but the hype cannot be beat.

1.) Pokemon Mystery Dungeon 2015 - Okay for real though I was not expecting this. My favorite game series of all time and it wasn't even on the digital event? Shame on you Nintendo, this reveal hyped me up at least. My goodness I know already I am gonna enjoy this game a ton.

What our your E3 Nintendo favorite moments. They're probably not a lot of them, but name your top 3

So do I answer the question in the title or in your post?? Because they are 2 very different answers

Super Mario Maker
Star Fox
More Yoshi

Metroid Prime Federation Force
Chibi Robo Zip Lash
Dr Mario Miracle Cure

Just Star Fox off the top of my head.  Basically didn't care about the other games or I already saw more than enough footage of the other games.

Mario Maker, Xenoblade, and SMT x FE

Zelda Tri Force Heroes
Metroid Prime Federation Forces
Yoshi Yarn

-Fire Emblem Fates: I'm really looking rorward to this title. I really hope some of the annoyances with it (specially the two version thing) are clarified before its release. It looks great and I'm sure it will play great.

-Youkai Watch. About time this game arrives to the west. I thought the would release it this summer. I hope it doesn't arrive between september-november, most games that interest me release during that period, I don't want to accumulate unplayed games.

-Pokemon Mystery Dungeon. I'll buy this one after the reviews, because the last PMD didn't live up to the other games. It's nice to see the game nonetheless.

Fire Emblem Fates
SMT x Fire Emblem
Yoshi Woolly World

Basically the games the I got most excited about were the ones we already knew about; hence the disappointed.

Star Fox was the real disappointment though: what they showed looks super easy and lame. I think I saw a max of 5 enemies on screen at once. Bullshit. I want Platinum levels of crazy.

It's almost as though they wanted to avoid scaring people off the game by making it look like a game for children.

It was a cowardly presentation.

1. SMT x FE (really liked the gameplay i saw at the treehouse-stream
2. Super Mario Maker (after the World Championships a must-have for me)
3. Xenoblade X (awesome new trailer)

If i had to chose a game developed outside of Nintendo's first and second party developers, i would say Fast Racing Neo. Exactly what i wanted to see when the game finally got shown.