This was VERY, VERY, VERY, VERY difficult, because technically New Leaf is tied with e+ as my favorite. New Leaf is my favorite on a handheld, and e+ on a console. Here's what makes e+ my favorite console. First, it was the first to allow picture taking on SD cards (I even use one of the ones I took in my thumbnail), second you see there in my thumbnail is Reset Center- yeah, that was the first time in the series that showed up, you also had the introduction of medicine and sick animals, you could go into their houses when they weren't home if they were in the same acre (same in every version of GC/64 though, but still), the side scrolling was soooo much a reminder of Zelda, the NES games, some holidays were American (the re-localized the US localized version), if you had space, you could add whoever you wanted into your town using their e-reader card at the fountain (despite popular belief this is only available in e+ and HHD). The fact that it used those e-reader cards! Sure, they were region locked, but still. Add whoever you wanted was such an awesome feature they didn't add back until HHD, and that's kind of a limited game. There's more songs, more fish, more bugs, it was a great console game, but too bad it's only available on a Japanese system.
For New Leaf, they added all the great things the prior ones did, and expanded on them. They took out some things I kind of miss, like Blathers going on and on- kind of wish they treated him like Kapp'n where you could skip it if you wanted, but if you didn't could still hear him. Next, and this I absolutely love, they took out those mid-town cliffs!!! The only cliffs in the game where you need to find a ramp is for the beach, which kind of also sucked because I liked going to the beach without having to go down a cliff.
No matter what, I guess every game will have something I don't like- I didn't make them, but as far as my favorite overall, New Leaf has to get it, simply because it has the ability to go with me everywhere I go, and I NEVER change the clock other than for DST, so if I miss something at home, I'm SOL, I can't go back and get it, giving the win to New Leaf since I have yet to miss an event thanks to its portability.