My favorite was the ACNL Puzzle League Mini-Game. I’ve always liked Puzzle League, and I was enthralled to see that ACNL has its own version of Puzzle League.
I also liked the new items first featured in Happy Home Designer.
Being able to shake trees with my net out lol it's the only way I have ever been able to catch a bee in New Leaf and it made looking for the furniture way less stressful! (Also the secret storage and HHD touch screen controls for decorating)
Getting the chance to try out new villagers, Splatoon villagers, Zelda villagers! The cute lil bird is my fav.
Though never really tried them out but planning too.
And having the SP's have their very own RVs and items, that was really cool. I like how if you missed the chance to buy something from say, Blanca, you had to wait till she came back again.
The Splatoon content.
Okay ignoring the obvious answer from me, the new minigames were pretty fun too, especially Puzzle League. I also appreciate the extra storage and the HHD decorating controls.
The amiibo update introduced numerous features and neat little easter eggs everywhere. Here's an example - some of my favorite additions are the campsite and the ability to scan amiibos through Wisp, which allows you to purchase exclusive items or even invite villagers to your town. One of the items you can order is a Wii U, and surprise, you can play a hidden mini-game like Desert Island Escape, which I also thoroughly enjoy (and is a reference to the NES in the original Animal Crossing... oh and there's Amiibo Festival, I guess). I love discovering stuff like this, uncovering it for the first time was such a treat.
Also, praise the secret storage, it's amazing. Thank you!