Retro and Retro inspired games
Ultimate NES Remix is fantastic. I 100%'d that game.
Sega 3D Classics Collection is pretty good. I bought most of them Digitally because that wasn’t available yet.
Shovel Knight and Mega Man Legacy Collection
Ocarina and Majora are my favorite versions of the games.
Action & Platformers
Kirby Planet Robobot is my favorite Kirby game since the SNES days
Super Mario 3D Land
Metroid Samus Returns is OK, I guess. I am only down on it because I loved AM2R infinitely more. I think the controls are not good and I didn’t care for the Melee as it was required in EVERY thing you did in the game.
Luigi’s Mansion Dark Moon really does a great job with 3D.
RPGs & Strategy
DQ7 & 8 if you are in the Dragon Quest games.
Bravely Default, its amazing the 1st time through but like Ghouls & Ghosts you are going to have to repeat it to beat it.
Fire Emblem series is great. I recommend Awakening because its a complete package but the other two games are legit.
Xenoblade Chronicles. Its one of the only games that takes advantage of the extra power in the New 3DS.
Radiant Historia - Its a port of an excellent DS game. Better production value. I highly recommend this one.
Mario & Luigi: Super Star Saga
Ever Oasis (from the creator of Secret of Mana games)
Codename Steam - Fire Emblem’s developer in this weird XCOM meets American Folklore where Abe Lincoln is fighting an Alien Invasion. Its been patched and the enemy’s turn is no longer annoying.
Rhythm Thief - Sega + Rhythm = Win
Fantasy Life - its a weird mix of rpg and Animal Crossing (oh yeah, Animal Crossing is Animal Crossing, if that is your thing).
Box Boy Series is really good
Ace Attorney Trilogy and Sequels
Shantae and the Pirate’s Curse (i think it got a physical copy)
Mighty Switch Force
Azure Striker Gunvolt (its on Switch, might as well get it there).
I left some of the things you already mentioned off the list but I think that is all I got. Hope that helps.