Okay what Nintendo can definitely release on an N64 classic:
-1080 Snowboarding
-Donkey Kong 64 - Nintendo will have the rights to this surely. Maybe they'll cut out the arcade port in it.
-Dr. Mario 64 - This never hit Europe, could be a mild curiosity?
-Excitebike 64
-F-Zero X
-Kirby 64: The Crystal Shards - Liked, but not a classic.
-Legend of Zelda: Ocarina - Gotta be.
-Legend of Zelda: Majora - Needs to be there too.
-Mario Golf - Could see this getting the axe, Mario Tennis is just more iconic.
-Mario Kart 64
-Mario Party 1, 2 and 3 - I think they might just put one on there, likely the first?
-Mario Tennis - Birth of Waluigi.
-Paper Mario
-Pilotwings 64
-Sin & Punishment - Takes the Earthbound/Star Fox 2 'curiosity' slot.
-Star Fox 64
-Super Mario 64
-Super Smash Bros.
-Wave Race 64
-Yoshi's Story
Depending on the whims of the Pokémon Company:
-Pokémon Snap - Could see this make the cut, it was also on Wii VC right?
-Pokémon Stadium 1 and/or 2 - Loses a lot of appeal without crossplay with Pokémon Red/Blue
-Pokémon Puzzle League - Never came to Japan, weirdly enough.
-...Hey, you Pikachu??? - Needs a mic, won't happen.
Japan-only releases they won't include:
-Animal Crossing
-Custom Robo & Custom Robo V2
Without Rare you're missing:
-Diddy Kong Racing - This is a weird one, can Rare/Microsoft block this?
-Perfect Dark - I think this one's too intertwined with Xbox now.
-GoldenEye 007 - not happening due to licensing.
-Mickey's Speedway USA - licensed game, won't happen.
-Jet Force Gemini - ...maybe if MS play ball? Not iconic though.
-Blast Corps - ...maybe? Not iconic enough either though.
-Banjo-Kazooie - Don't see it happening sadly, probably the second-biggest loss.
-Banjo-Tooie
-Conker's Bad Fur Day - Would be hilarious if only this of the Rare games made it.
-Killer Instinct Gold - Xbox One launched with a version of this right? Don't think many will miss it.
Third party additions I could see happen:
-Bomberman 64 - Was on Wii U eShop. Konami has a lot on N64 but how willing they'd be?
-Castlevania 64 - Again, up to the whims of Konami. They might wanna keep this one dead.
-Ogre Battle 64: Person of Lordly Caliber - this came to virtual console twice, must be a good relationship.
-Harvest Moon 64 - Came to virtual console on Wii U, Natsume wants to keep this brand relevant.
-Rayman 2 - Ubisoft puts this on everything if it can.
-Ridge Racer 64 - Was internally developed & published by Nintendo I think?
Does Nintendo have rights to Argonaut games? Buck Bumble was published by Ubisoft...
Conclusion: Nintendo has ~20 games if it puts everything it has on one. That's acceptable (NES mini had 30, SNES just 21). Without Rare though there's not a single FPS, and there's just one RPG if Ogre Battle doesn't work out. No puzzle games unless either Dr. Mario or Pokémon Puzzle League makes it; both were regional exclusives. No fighting game besides Smash Bros.
I thought it would look worse tbh, but there's still many titles people associate with N64 that aren't here: Cruisin' USA, Turok, Star Wars, Top Gear Rally, Tony Hawk, none of the sports/wrestling titles, and obviously Rare's contributions. No crappy 3D fighters sadly, and honestly not very many 3D platformers unless they get Banjo and/or Rayman.
I think they can stand to miss a few of those for sure, but GoldenEye and Banjo-Kazooie are the most obvious losses.