It's likely that the 3DS has similar issues running the SNES as it does with the GBA, which is why it's not got Virtual Console titles. If memory serves, there are a couple of SNES games that have been put on the 3DS somehow, but I believe they were ported, not Virtual Console'd.
The next console/handheld will be different. New account system is coming this autumn, will tie stuff together and Iwata talked about the handheld and home console sharing architecture (with different specs) and absorbing the Wii U architecture. I believe there was talk of VC being there at launch with a large amount of titles (but that might have been a dream) due to that. So it won't be an issue much longer
That list is outdated and slightly incorrect (Yoshi's Cookie actually has licensing issues and The Mysterious Murasame Castle definitely has a chance since I released on 3DS). I would like to see a more up-to-date version with Wii games included.
Well that post was in September
NES
F-1 Race - Unlikely due to license
Wild Gunman
Hogan's Alley
Kung-Fu Master - Unlikely due to the license (was based on a Jackie Chan movie)
Stack-up - Unlikely due to needing R.O.B.
Gyromite - Unlikely due to needing R.O.B.
Gumshoe
Nazo no Murasame Jo - Japan only
Pro Wrestling
Slalom - Actually unsure about this. Was made by Rare.
Famicom Grand Prix: F1 Race - Japan Only
Famicom Grand Prix II: 3D Hot Rally - Japan Only
R.C. Pro-Am - Same as Slalom
Famicom Wars - Japan Only
Tetris - Licensing
Famicom Detective Club: The Missing Heir - Japan only
Cobra Triangle - Same as Slalom
Mother - Japan Only
Barker Bill's Trick Shooting - Licensing issues
NES Play Action Football - North America only
Star Tropics
Snake Rattle 'n' Roll - Same as Slalom & Mattel Licensing issues
Pin-Bot - Same as Slalom
Nintendo World Cup - Japan Only
Time Twist: On the Outskirts of History... - Japan Only
Fire Emblem: Shadow Dragon and the Blade of Light - Japan Only
Fire Emblem Gaiden - Japan Only
Yoshi's Cookie - Weird Licensing Issues
Joy Mech Fight - Japan Only
Zoda's Revenge: StarTropics II
Total remaining eligible first party titles outside Japan: 5
SNES
SimCity - Will never happen. Got removed off the Wii Virtual Console due to EA.
Mario Paint - Unlikely (Mouse required)
Super Scope 6 - Unlikely (Super Scope required)
Battle Clash - Unlikely (Super Scope required)
Super Play Action Football - NA Only. Unlikely due to license
World League Basketball - Unlikely due to license
StarFox - Super FX chip makes it unlikely
Yoshi's Safari - Unlikely (Super Scope Required)
Super Mario All-Stars - I don't think this is likely, unfortunately
Metal Combat: Falcon's Revenge - Unlikely (Super Scope Required)
Super Hockey - Unlikely due to license
Super Tennis
Mario & Wario - Unlikely (Japan only and Mouse required)
Stunt Race FX - Super FX chip makes it unlikely
Tin Star - North America Only
Ken Griffey, Jr. Presents Major League Baseball - NA Only. Unlikely due to license
Uniracers - Not going to happen due to lawsuit by Pixar
Wario's Woods - We got the NES version
Fire Emblem: Mystery of the Emblem - Japan only
Super Mario World 2: Yoshi's Island - Super FX chip makes it unlikely
Kirby's Ghost Trap
Super Mario RPG (Requires Square Enix to pull their foot out)
Ken Griffey, Jr.'s Winning Run - Unlikely due to license
Tetris Attack - Though Tetris moniker may make it unlikely.
Kirby's Star Stacker
Wrecking Crew '98 - Japan only. Unlikely.
Super Famicom Wars - Japan only
Sutte Hakkun - Japan Only
Fire Emblem: Thracia 776 - Japan only
Total remaining eligible first party titles outside Japan: 5
GBA
Super Mario Advance (Japan got it)
Kuru Kuru Kururin
Magical Vacation - Japan only
Disney's Magical Quest Starring Mickey & Minnie - Unlikely (License)
Game & Watch Gallery 4
The Legend of Zelda: A Link to the Past/Four Swords
Super Mario World: Super Mario Advance 2 (Japan/US got it)
Tomato Adventure - Japan only
Domo-Kun no Fushigi Terebi - Japan only
Koro Koro Puzzle Happy Panechu! - Japan only
Fire Emblem: Fuin no Tsurugi - Japan only
Sakura Momoko no Ukiuki Carnival - Japan only
Custom Robo GX - Japan only
Densetsu no Stafy - Japan only
Kururin Paradise - Japan only
Advance Wars 2: Black Hole Rising
Donkey Kong Country
Final Fantasy Tactics Advance (Requires Square Enix)
Hamtaro: Ham-Ham Heartbreak (Licensing)
Hamtaro: Rainbow Rescue (Licensing)
Pokémon Ruby and Sapphire - Never going to happen
Super Mario Advance 4: Super Mario Bros. 3
Sword of Mana (Requires Square Enix)
Top Gear Rally - Unlikely due to licensing
Mother 1 + 2 - Japan only
Densetsu no Stafy 2 - Japan only
Donkey Kong Country 2
Final Fantasy I & II: Dawn of Souls (Requires Square Enix)
Hamtaro: Ham-Ham Games (Licensing)
Mario vs. Donkey Kong
Pokémon FireRed and LeafGreen - Not going to happen
Densetsu no Stafy 3 - Japan only
F-Zero Climax - Japan only
Donkey Kong Country 3
Dr. Mario & Puzzle League
Dynasty Warriors Advance - Requires Tecmo Koei
Final Fantasy IV Advance - Requires Square Enix
Fire Emblem: The Sacred Stones (US Got it)
Pokémon Emerald - Not going to happen
WarioWare: Twisted! - Tilt control could make it tricky
Yoshi Topsy-Turvy - Tilt control could make it tricky
Sennen Kazoku - Japan only
Nonono Puzzle Chalien - Japan only
Drill Dozer
Pokémon Mystery Dungeon: Red Rescue Team
Eyeshield 21: Devilbats Devildays - Japan only
Mother 3 - Japan only
Calciobit - Japan only
Total remaining eligible first party titles outside Japan: 11
Wii
Wii Sports
Excite Truck
The Legend of Zelda: Twilight Princess
WarioWare: Smooth Moves
Wii Play
Super Paper Mario
Mario Party 8
Big Brain Academy: Wii Degree
Pokémon Battle Revolution
Mario Strikers Charged
Metroid Prime 3: Corruption
Donkey Kong Barrel Blast
Battalion Wars 2
Fire Emblem: Radiant Dawn
Super Mario Galaxy
Link's Crossbow Training
Eyeshield 21: The Field's Greatest Warriors - Unlikely (Japan only)
Endless Ocean
Super Smash Bros. Brawl
Mario Kart Wii
Wii Fit
Mario Super Sluggers
Wario Land: Shake It!
Wii Music
Animal Crossing: City Folk
Wii Chess
Minna no Joushiki Ryoku TV - Unlikely (Japan only)
Zero: Tsukihami no Kamen - Unlikely (Japan only)
Captain Rainbow - Unlikely (Japan only)
Disaster: Day of Crisis
New Play Control! Mario Power Tennis
New Play Control! Pikmin
Excitebots: Trick Racing
New Play Control! Donkey Kong Jungle Beat
Wii Sports Resort
Metroid Prime: Trilogy
Wii Fit Plus
New Super Mario Bros. Wii
Another Code: R – A Journey into Lost Memories
Takt of Magic (Japan only)
New Play Control! Chibi-Robo - Unlikely (Japan only)
Minna ga Shuyaku no NHK Kouhaku Quiz Kassen - Unlikely (Japan only)
Endless Ocean: Blue World
Sin & Punishment: Star Successor (Out in Japan)
PokéPark Wii: Pikachu's Adventure
Metroid: Other M
Wii Party
Kirby's Epic Yarn
Super Mario All-Stars 25th Anniversary Edition - I see it as unlikely
Zangeki no Reginleiv- Unlikely (Japan only)
Ando Kensaku- Unlikely (Japan only)
Mario Sports Mix
Wii Play: Motion
The Legend of Zelda: Skyward Sword
Fortune Street - Would require Square Enix
Rhythm Heaven Fever
PokéPark 2: Wonders Beyond
Mario Party 9
Xenoblade Chronicles - Unlikely thanks to 3DS version
New Play Control! Pikmin 2
Kirby's Dream Collection
The Last Story
Project Zero 2: Wii Edition
Kiki Trick (Japan only)
Pandora's Tower
Total remaining eligible first party titles outside Japan: 50
HYPOTHETICALS
N64
Super Mario 64
Pilotwings 64
Shadows Of The Empire - Licensing
Cruis'n USA - Licensing
Killer Instinct Gold - Rare
Wave Race 64
Mario Kart 64
Mischief Makers - Don't own the rights
Bomberman 64 - Don't own the rights
Blast Corps - Rare
Star Fox 64
GoldenEye 007 - Never going to happen
Tetrisphere
Diddy Kong Racing - Rare
Yoshi's Story
1080° Snowboarding
F-Zero X
Bomberman Hero - Don't own rights
Kobe Bryant in NBA Courtside - Licensing
Banjo-Kazooie - Rare
Major League Baseball Featuring Ken Griffey, Jr. - Licensing
Waialae Country Club: True Golf Classics - Licensing
Mario Party
Cruis'n World - Don't own the rights
Pocket Monsters' Stadium - Won't happen
The Legend of Zelda: Ocarina of Time
Hey You, Pikachu! - Mic Issues
Pokémon Snap
Custom Robo
Mario Golf
Pokémon Stadium
Super Smash Bros.
Donkey Kong 64 - Iffy
Jet Force Gemini - Rare
Command & Conquer 64 - Don't own rights
NBA Courtside 2: Featuring Kobe Bryant - Licensing
Ken Griffey, Jr.'s Slugfest - Licensing
The New Tetris
Mario Party 2
Ridge Racer 64- Don't own rights
Mario Tennis
The Legend of Zelda: Majora's Mask
Pokémon Puzzle League
Kirby 64: The Crystal Shards
Excitebike 64
Perfect Dark - Rare
Banjo-Tooie - Rare
Custom Robo V2
Pokémon Stadium 2
Paper Mario
Mickey's Speedway USA - Licensing
Sin & Punishment
Mario Party 3
Dr. Mario 64
Animal Crossing
Total remaining eligible first party titles outside Japan: 27
Knowing that most likely they will abandon their curent powerPC architecture for their next home console since they are looking into having a common OS with their next handheld; then their current VC effort will also most likely have to be rebuilt from scratch. Therefore I wouldn't be surprised if that's one of the reason that they don't invest too much into current Wii U VC.
They said that NX is said to absorb the Wii U architecture, so we should be set