Let's say 15.
1) Mario 64 - It's a little-known game, but I think Nintendo may want to give it a chance.
2) Ocarina of Time - Majora's Mask would be on here as well, but there's the one-per-series rule (tbh I think Nintendo would include both of them). Maybe Master Quest could be the "bonus" title a la Star Fox 2.
3) Donkey Kong 64 - Whatever arrangement they have with Rare has already let them do this as a Virtual Console title so I'd consider it a shoe-in.
4) Paper Mario - N64 is weak on traditional RPGs and this is easily the most well-known.
5) Star Fox 64 - After two Star Fox games made it into the SNES Classic this seems like a no-brainer.
6) Super Smash Bros. - I don't think this series ever really hit it big until Melee, but the first game still sold well and is fun in its own right.
7) Mario Kart 64 - tbh my least favorite of the console Mario Karts, but it's a staple of the library.
8) Mario Party 2 - Almost has to be represented, and this one seems to be the go-to for Nintendo (1 has the joystick issue, 3 has never been rereleased to my knowledge).
9) Kirby 64: The Crystal Shards - Just gotta get all those big Nintendo franchises represented.
10) Mario Golf - I feel the N64 era was where Nintendo really started overexposing Mario in every genre.
11) Mario Tennis - oh god so much Mario
12) Wave Race 64 - Never played it myself but it seems to be fairly beloved, enough to get a sequel on the GameCube at launch.
13) Pokémon Snap - I imagine Pokémon would be represented on here somehow, but Hey You, Pikachu is obviously out, and the Stadium games require the transfer pak to get the most of it (playing with rentals would suuuck) which means it would come down to Snap or Puzzle League. I'm guessing they'd go with Snap just because it seemed to be more popular, but who knows. If they could somehow finagle it to let you upload Pokémon from the 3DS Virtual Console games, I'd rather they do Pokémon Stadium 2.
14) F-Zero X - Almost forgot about this one! Sorry F-Zero, you know I love you baby.
15) Sin and Punishment - It's been a mainstay release for every Virtual Console N64 lineup, so I imagine it would find its way here as an easy "look, a game we never released in America!*"
Swap out the Mario sports games for Majora's Mask and 1080 Snowboarding if preferred.
Bonus, third party deals!
16) Castlevania 64 - This game isn't very highly esteemed, but I could see Nintendo including it for brand recognition.
17) Mega Man 64 - Same as Castlevania. One more name they could slap on the box.
18) Star Wars: Rogue Squadron - I think Shadows of the Empire is more iconic to the N64 being a launch window title, but Rogue Squadron has aged much better.
19) Banjo-Kazooie - One of the biggies, obviously this would require some wheeling and dealing with Microsoft to get this done, but probably an easier lift than...
20) GoldenEye 007 - If they didn't want to deal with the licensing kerfuffle, they could always go with Perfect Dark, but I think Nintendo would shy away from including anything M-rated just so kids aren't prevented from buying the console.
21) Bonus Unreleased Game Wow: Dinosaur Planet - lol