Well if this thing is actually running on some modified 3DS hardware, the missing Nintendo published games from 3DS VC are NES Open Golf, Super Mario 2 JP, Yoshi, Wrecking Crew, Wario's Woods, Donkey Kong 3, Clu Clu Land, Mach Rider, The Mysterious Murasame Castle, and Adventures of Lolo.
None of those seem like huge misses for a product that is meant to invoke nostalgia.
Wrecking Crew and Golf would at least match some of the stuff that's already on the NES Mini in terms of nostalgia, but neither are huge losses. Wario's Woods, as a puzzle game, holds up a bit better than some other stuff, but it's not really worth it. The real Mario 2 is not great for nostalgia purposes in the US, but is actually relatively famous and was included in its easymode in Super Mario All-Stars, which everyone who had an SNES remembers. I could see sticking the original Mario 2 on there, but I understand why they didn't.
I kind of wish they had stuck some Dragon Warrior games on there, given that SE was clearly on board in giving them Final Fantasy, but Dragon (Quest) Warrior I-IV NES version were absolutely brutal slogs that became much more playable in their remakes. Dragon Warrior IV NES is one of the most impressive titles on the NES, though, so it might've been a worthwhile thing to stick on.
If nostalgia weren't a requirement, sticking Earthbound Beginnings on there would also be a good idea, but that game is
hard.
There's also an official SE translation of Final Fantasy II NES that they didn't end up releasing because it was at the very end of the NES' lifespan so they decided not to release it. Again, it's probably not a game that would be good for something like this and would just alienate people due to its extreme obtuseness and difficulty. It's a shame the Famicom Final Fantasy III doesn't have an English version because that game
does hold up far better than Final Fantasies I or II do and is legitimately hugely impressive for an NES game.
It's a shame there's no English version of the NES/SNES Fire Emblem games, but that ship sailed decades ago.