I am pulling this from my ass but, if a successful game is made, who gets the credit? Who gets the money? Would the "indie" company demand more next time? Could they take Nintendo's ideas and sell them?

Like Thanos, I'd put on the infinity gauntlet and say "I'll do it myself."

Yea, it's pretty much those three among other reasons. Indies can't simply hire 100 more people to make these games. Heck, the team behind FAST Racing isn't really a big team. Then also the potential to sell. You can't just slap the name Star Tropics and expect decent sales just because some fans wanted a new game. And in general, I'm sure internally, Nintendo has thought about using old IPs not used often. That's why Pilotwigs, Kid Icarus, Sin and Punishment, and Punch Out! got games over the past several years. It would be great if indies could handle some of Nintendo's other IPs, if it's possible.

If they need to all that trouble to outsource an IP (and that still wouldnt resolve the manpower issue), I think it just would be easier to go to a bigger company instead.

Image&Form has also said they wants to create a 2D Metroid game.

Number of employees has nothing to do with whether they're an indie developer or not. If they're a company that is not owned by anyone, and is run INDEPENDENTLY, they're an indie dev.

Good-Feel and Next Level Games are quite clearly not independently run.

And your definition is wrong as well. Every company is owned by someone. Even indie developers need to listen to the demands of publishers. Using your definition Nintendo is an indie developer. 

Budget, most indie devs could commit very little in the way of funds so for Nintendo there is little financial incentive on that end.

Scale, the majority of indie devs are fery compact teams and not structured for working with publishers and overseers on very large projects.  Most would drown in such a partnership. Of course you could leave them to their devices but that leads to...

Risk: most indies work best out from under publishers/overseers. Which means for this to work you would have to roll the dice that the dev gets it right. Most 1st parties don't want to do that.

Honestly, very few indies would work well as part of such a partnership. Maybe Shin'en and Playtonics, maybe.

They are really protective of their IP and don't want it in the wrong hands, would be my guess. Don't want to 'taint' their IP with bad games and want control over development

That said, giving Shin'en F-Zero would just make sense :p

Sonic Mania.

Except they are technically still independent. Yes, they work exclusively with Nintendo, but Nintendo has no stake in them. They don't own any part of them. They've just decided to work with them and make games for them.

I don't think you understand what "owning" means. Having an outside publisher publish your game doesn't mean they own the team. It's a partnership that may only last one game and then they could part ways. That publisher never owns them. They don't have control of the company at any point. Bioware is owned by EA. Naughty Dog is owned by Sony. Retro is owned by Nintendo. Next Level is not owned by Nintendo. Obsidian is not owned by Bethesda or Ubisoft. They're both technically independent.

As long as another company doesn't own you, and probably if you don't own any companies yourself, you're technically independent.