I want Paper Zelda as a comedy RPG and Duck Hunt to get a reboot as a strategic TPS ala Garden Warfare

This is a fantastic idea...

In multiplayer you play as either Ulyaoth, Xel'lotath, or Chattur'gha...

In the single player campaign you play as Mantorok and you have to keep the other three in check...

On a different note, I think a Metroid spinoff where you play the entire game in Morph Ball Mode could be pretty cool...

Solve puzzles, get different types of bombs, find different ways to kill enemies, all while spinning through subterranean tunnels or giant machines or pipes...

I believe Federation Force could work as an online Fps with great graphics and Metroid Prime artstyle.

How about a turn based zelda rpg in the same vein as dragon quest.That would be great i'd prefer it over those top down zelda games like phantom hourglass, spirit tracks etc.

The legend of paper Zelda.... anyone?

LEGO Legend of Zelda seems like it would be a lot of fun to me.
Wario & Waluigi: Kingdom Battle
Maybe a dungeon crawler or 'traditional' i.e. non-strategy RPG based on Fire Emblem, though I'd rather see Golden Sun rebooted.
Paper Luigi - based on his adventures during Thousand Year Door.

Not quite a Nintendo spin-off, but a game set in the Game of Thrones/Song of Ice and Fire universe but which plays like Fire Emblem would be right up my street. Maybe call it Thrones Emblem and get Intelligent Systems to make it.

Super Smash Bros.: Battle Royale

I have always wished for such a game. F-Zero has a semi super hero based quirky lore that really was never touched outside of manuals and a anime that is better left alone. A game like that would be awesome and might be the jump start the franchise needs beyond its excellent game play .

Also a Splatoon rhythm game in style of Elite Beat Agents.

Star Fox spin off based around the Landmaster/tank and featuring a different protagonist in the same universe by Platinum Games

Edit: Also while I doubt Nintendo has interest if they ever wanted to make a strategy game the Kid Icarus franchise after Uprising has enough characters,  potential factions and disposable foot soldiers to work. Heck if they wanted it could be tweaked into a MOBA.

Elite Squid Agents? I already see Callie and Marie dancing in the missions and their Grandpa pointing the Finger: Agents are GO!!!

1. Princess of Hyrule:
A LoZ Spin-Of with gameplay like the Prince of Persia series. Zelda will be the playable Character
and the rough plot will be Zelda trying to escape her predetermined life as a Princess while dark force trying to destroy Kingdom Hyrule.

Pokémon RPG:
A Pokémon game with decent Story and interesting gameplay outside of fights.
Jokes aside. That's less an idea for a Spin-Of and more what I would love to see from every Pokémon game.
Real Quests and Dialoges with different branches,
Your Pokémon should be able to interact with the Gameworld a lot more and It should actually matter what Pokémon you're catching for example:
You have to gain access to a control room. You have three different options. a) find the replacement key for the door to the control room, b) use a Pokémon with hypnosis to get the guard to unlock the door or c) use the Pokémon Klefki as a key.

about the story, I don't want a Pokémongame with a dark and gritty story, there are plenty of good examples out there for stories that are enjoyable for both kids and adults they just needs to hire good Authors and give them enough time and freedom for a good story.

3. GTSquid:
Crossover between Splatoon and Saints Row