So I think I might get these:
Zelda: ALBW
Animal Crossing New Leaf
Super Mario 3D Land
Paper Mario Stciker Star
Theaterhythm CC
Kid Icarus Uprising
Monster Hunter 4 Ultimate (Forgot to mention I love the Monster Hunter series)
Phoenix Wright
Fire Emblem Awakening
Luigi's Mansion Dark Moon
Mario and Luigi Paper Jam
Final Fantasy Explorers
Out of that list, put Paper Jam over Sticker Star, if at all - I personally would scratch both, as long as you have enough other games to play (which seems to be the case). I will go out of my way to even claim you should get Fantasy Life instead before getting any of the Mario RPGs. They are really just very average.
New Leaf and ALBW are the rightful top 2 here I think.
Definitely put Fire Emblem Awakening higher on the list though - there is a demo on the eshop too, so check it out to convince yourself.
The next best JRPG is Bravely Default, but it has some major flaws (which will only become apparent about 20 hours into the game, so I still recommend it).
The rest of the list is extremely solid, but I think Rhythm Thief and Harmoknight might be more your thing if you liked Elite Beat Agents over Theathrythm - but Theathrythm has FF music, so there's that. (I am addicted to Theathrythm, so that is not meant to put the game down!) I also played the Miku game, but hated it - it has a one time demo (lol) on the eshop, so you can see for yourself.
Hey, if you end up liking Phoenix Wright (which I really hope), the next best things on the 3DS are Ghost Trick (DS) and 999 (DS) + VLR (3DS). The visual novel thing is not for everyone, but people usually enjoy it a lot more than they thought they would. There are some more DS games like that, but yeah, check Phoenix Wright out as a start.
As an Animal Crossing connaisseur, how about some Harvest Moon? Just don't pick the ones with Harvest Moon in the name: You will enjoy Story of Seasons and Rune Factory 4 a lot more.
Also, do not dismiss the eshop. Shovel Knight is the real Mario you are looking for (well, it would be, if 3D Land was not as good as it is... but Shovel Knight will still be to your liking). It should even come out for retail though, so you can stay off digital if that is the reason you dismissed the game.
Stay away from the Free-To-Start stuff with Pokémon - the Badge Center and Steel Diver Sub Wars are the only free games that actually feel gamey. (Personal preference and all, but the Pokémon Games have these really horrible paywalls sooner or later, I felt they were simply frustrating.)
Have fun, and don't start building a backlog just yet - once the new account system hits in March, you might profit off of buying your stuff much more, like when they used to give extra codes for a specific amount of eshop purchases, or the Club Nintendo point system with the codes from retail purchases.
So: Don't buy a lot of stuff now, only to realize you could have gotten cool gifts from those purchases once the new account system starts.