Oh and light gun games:

Barke Bill's Trick Shooting
Hogan's Alley
Gumshoe

They have a ridiculous amount of IPs. Holy shit.

Punch Out for fighter game

Cruis'n USA Cruis'n World

Here are some IP I think you missed.  I apologize in advance if there are any repeats, because both of our lists are quite long.

Nintendo arcade games:
https://nintendo.fandom.com/wiki/List_of_Nintendo-related_arcade_games

EVR Race (Guessing)
Shooting Trainger (Flash Gun)
Test Driver (Driving Simulator)
Block Fever (Block Breaking)
Space Fever (Shmup)
Space Launcher (???)
Monkey Magic (Block Breaking)
Space Firebird (Shmup)
Radar Scope (Shmup)
HeliFire (Shmup)
Sky Skipper (Shmup)
Space Demon (Shmup)
Arm Wrestling (Sports)
Popeye? (Maze – not sure of legalities of this)

Here are some games you have (partially), but I think need more entries:
Donkey Kong
Donkey Kong Jr
Donkey Kong Country (I feel these are 3 separate IP)

Mario Bros (platformer)
Super Mario (2D)
Super Mario (3D)
Mario vs Donkey Kong (Puzzle)

Excite_____ (Racing)
(the second part could be bike, truck or bots)

Here are some other IP I think you missed:
Diddy Kong Racing (Racing)
Wii Fit (Exercise)
Wii Party (Party)
Wii Music (Rhythm)
Fling Smash (???)

Not sure if Nintendo owns these IP:
Elite Beat Agents (Rhythm)
Snipperclips (Puzzle)
Good Job! (Puzzle)

Off the top of my head:

Art Academy, Hamtaro, Fossil Fighters, Donkey Konga, Starfy, Harmoknight, Labo, Band Brothers, Denpamen, Teleroboxer, Yoshi's Safari, Nester's Funky Boxing, Doshin the Giant, Mickey's Speedway USA, Art Style ___.

Here's a list of every Nintendo franchise listed by platform of release, copied from another website, circa early 2015.

<Arcade (~)> (19)
Wild Gunman (1974)
EVR Race (1975)
Sky Hawk (1976)
Battle Shark (1977)
Test Driver (1978)
Block Fever (1978)
Computer Othello (1978)
Space Fever (1979)
Space Launcher (1979)
Sheriff (1979)
Monkey Magic (1979)
Head On N (1979)
Radar Scope (1979)
Space Firebird (1980)
HeliFire (1980)
Donkey Kong (July 1981)
Sky Skipper (1981)
Mario Bros. (July 1983)
Punch-Out!! (1984)

<Color TV-Game (1977)> (5)
Color TV-Game 6 (1977)
Color TV-Game 15 (1978)
Color TV-Game Racing 112 (1978)
Color TV-Game Block Breaker (1979)
Computer TV-Game (1980)

<Computer Mahjong (?)> (1)
Computer Mahjon (?)

<Game and Watch (April 1980)> (29)
Ball (April 1980)
Flagman (June 1980)
Vermin (July 1980)
Fire (July 1980)
Judge (October 1980)
Manhole (1981)
Helmet (February 1981)
Lion (April 1981)
Parachute (June 1981)
Octopus (July 1981)
Chef (September 1981)
Egg (October 1981)
Turtle Bridge (February 1982)
Fire Attack (1982)
Oil Panic (May 1982)
Green House (December 1982)
Rain Shower (1983)
Lifeboat (October 1983)
Pinball (December 1983)
Spitball Sparky (February 1984)
Crab Grab (February 1984)
Boxing (July 1984)
Black Jack (1984)
Tropical Fish (July 1985)
Squish (April 1986)
Climber (1986)
Bombsweeper (June 1987)
Safebuster (1988)
Gold Cliff (October 1988)

<Famicom (July 1983)> (26)
Gomoku Narabe Renju (August 1983)
Mahjong (August 1983)
NES Sports (December 1983)
Pinball (February 1984)
Duck Hunt (April 1984)
Hogan's Alley (June 1984)
Devil World (October 1984)
F-1 Race (November 1984)
Urban Champion (November 1984)
Clu Clu Land (November 1984)
Excite (November 1984)
Balloon Fight (January 1985)
Ice Climber (January 1985)
Stack-Up (July 1985)
Gyromite (August 1985)
Mach Rider (October 1985)
Gumshoe (June 1986)
Glory of Heracles (June 1987)
Wars (August 1988)
Mother (July 1989)
To the Earth (November 1989)
Short Order + Eggsplode (December 1989)
Fire Emblem (April 1990)
Play Action Football (September 1990)
StarTropics (December 1990)
Joy Mech Fight (May 1993)

<Famicom Disk System (February 1986)> (10)
Legend of Zelda (February 1986)
Mysterious Murasame Castle (April 1986)
Metroid (August 1986)
Kid Icarus (December 1986)
Shin Onigashima (September 1987)
Famicom Grand Prix (October 1987)
Nakayama Miho no Tokimeki High School (December 1987)
Famicom Tantei Club (April 1988)
Yuyuki (October 1989)
Time Twist: Rekishi no Katasumi de... (July 1991)

<Game Boy (April 1989)> (18)
Alleyway (April 1989)
Yakuman (April 1989)
Solar Striker (January 1990)
Radar Mission (October 1990)
Yoshi (December 1991)
Kirby's Dream Land (April 1992)
X (May 1992)
Wave Race (July 1992)
Kaeru no Tame ni Kane wa Naru (September 1992)
Top Rank Tennis (May 1993)
Wario Land (January 1994)
Game & Watch Gallery (April 1995)
Pokémon (February 1996)
Mole Mania (July 1996)
Trade & Battle: Card Hero (February 2000)
Warlocked (July 2000)
Karkurenbo Battle Monster Tactics (November 2000)
Mobile Golf (May 2001)

<Super Famicom (November 1990)> (16)
F-Zero (November 1990)
Pilotwings (December 1990)
SimCity (April 1991)
Super Scope 6 (February 1992)
Battle Clash (October 1992)
Star Fox (February 1993)
Vegas Stakes (May 1993)
Stunt Race FX (June 1994)
Ken Griffey Jr. Presents Major League Baseball (March 1994)
Tin Star (November 1994)
Uniracers (December 1994)
Panel de Pon (October 1995)
Marvelous: Mouhitotsu no Takarajima (October 1996)
Zoo-tto Mahjong! (July 1998)
Picross NP (April 1999)
Famicom Bunko: Hajimari no Mori (July 1999)

<Satellaview (April 1995)> (4)
Special Tee Shot (January 1996)
Itoi Shigesato no Bass Tsuri No. 1 (February 1997)
Sutte Hakkun (November 1997)
Satella Walker (Unknown)

<Virtual Boy (July 1995)> (4)
Galactic Pinball (July 1995)
Red Alarm (July 1995)
Teleroboxer (July 1995)
Nester's Funky Bowling (February 1996)

<Nintendo 64 (June 1996)> (6)
1080° (February 1998)
Super Smash Bros. (January 1999)
Custom Robo (December 1999)
Doshin the Giant (December 1999)
Sin and Punishment (November 2000)
Animal Crossing (April 2001)

<Game Boy Advance (March 2001)> (11)
Kururin (March 2001)
Golden Sun (August 2001)
Magical Vacation (December 2001)
Tomato Adventure (January 2002)
Koro Koro Puzzle Happy Panechu (March 2002)
Sakura Momoko no Ukiuki Carnival (July 2002)
The Legendary Starfy (September 2002)
Sennen Kazoku (March 2005)
Drill Dozer (September 2005)
Calcio Bit (May 2006)
bit Generations (July 2006)
Rhythm Heaven (August 2006)

<Nintendo Gamecube (September 2001)> (8)
Pikmin (October 2001)
Cubivore (February 2002)
Eternal Darkness (June 2002)
GiFTPiA (April 2003)
Chibi-Robo (June 2005)
Geist (August 2005)
Densetsu no Quiz Ou Ketteisen (December 2005)
Odama (March 2006)

<Nintendo DS (November 2004)> (42)
Jam with the Band (December 2004)
Polarium (December 2004)
Trace Memory (February 2005)
Electroplankton (April 2005)
Nintendogs (April 2005)
Brain Age (May 2005)
Rakubiki Jiten (June 2005)
Ouendan (July 2005)
Clubhouse Games (November 2005)
Magnetica (March 2006)
Big Brain Academy (June 2005)
English Training (January 2006)
Tabi no Yubisashi Kaiwachou DS (April 2006)
Mawashit Tsunageru Touch Panic (May 2006)
Project Hacker (July 2006)
Cooking Navi (July 2006)
Chosoju Mecha MG (September 2006)
Tingle (September 2006)
Kanshū Nippon Jōshikiryoku Kentei Kyōkai: Imasara Hito ni wa Kikenai Otona no Jōshikiryoku Training DS (October 2006)
Master of Illusion (November 2006)
Kenkou Ouen Recipe 1000: DS Kondate Zenshuu (December 2006)
Touch Hyakunin Isshu: DS Shigureden (December 2006)
Hotel Dusk (January 2007)
Personal Trainer: Math (January 2007)
Jet Impulse (February 2007)
Kurikin: Nano Island Story (May 2007)
Flash Focus (May 2007)
Suujin Taisen (June 2007)
Ganbaru Watashi no Kakei Diary (July 2007)
Face Training (August 2007)
Slide Adventure MAGKID (August 2007)
theta (September 2007)
Zekkyō Senshi Sakeburein (September 2007)
ASH: Archaic Sealed Heat (October 2007)
Make 10: A Journey of Numbers (October 2007)
Soma Bringer (February 2008)
Fossil Fighters (April 2008)
Crosswords DS (May 2008)
Style Savvy (October 2008)
DS Uranai Seikatsu (January 2009)
Tomodachi Life (June 2009)
Active Health (August 2009)
Art Academy (June 2010)

<Wii (November 2006)> (11)
Wii (November 2006)
Endless Ocean (August 2007)
Minna no Joushiki Ryoku TV (March 2008)
Captain Rainbow (August 2008)
Disaster: Day of Crisis (September 2008)
Takt of Magic (May 2009)
And-Kensaku (April 2010)
FlingSmash (November 2010)
Xenoblade Chronicles (June 2010)
The Last Story (January 2011)
Pandora's Tower (May 2011)

<WiiWare (March 2008)> (11)
MaBoShi: The Three Shape Arcade (August 2008)
PictureBook Games (March 2009)
Rock N' Roll Climber (August 2009)
You, Me and the Cubes (September 2009)
Grill-Off with Ultra Hand! (November 2009)
Eco Shooter: Plant 530 (November 2009)
Line Attack Heroes (July 2010)
AquaSpace (July 2010)
ThruSpace (October 2010)
Snowpack Park (November 2010)
Fluidity (December 2010)

<DSiWare (November 2008)> (2)
Flipnote Studio (December 2008)
Looksley's Line Up (March 2010)

<Nintendo 3DS (Feb 2011)> (10)
Steel Diver (March 2011)
Freakyforms (September 2011)
Pushmo (October 2011)
Sakura Samura (November 2011)
Spirit Camera (January 2012)
Dillon's Rolling Western (February 2012)
HarmoKnight (September 2012)
Fantasy Life (December 2012)
Rusty's Real Deal Baseball (August 2013)
Codename: STEAM (Unreleased 2015)

<Wii U (November 2012)> (5)
Nintendo Land (November 2012)
SiNG Party (November 2012)
The Wonderful 101 (August 2013)
NES Remix (December 2013)
Splatoon (Unreleased 2015)

Sorry I didn't post that earlier, but I forgot about it.

Strategy has 2 sub-genre: turn based and realtime. Advance war is turn based strategy only, not rpg.

Codename Steam and Fire Emblem have the same genre: tactic rpg.

I am not sure if Bayonetta should be included on this list, but it currently doesn't appear to be listed. I read online that this IP is currently jointly owned between Nintendo and Sega. That said, Nintendo is only part owner in the Pokemon IP and that is on this list and so I am not sure if we are including IP that Nintendo jointly owns or only IP that is fully owned by Nintendo.  I just thought that I would throw it out there for discussion.

Very impressive list, though. I really cannot think of much else that might be missing from it.