And?  You asked for reasons, I gave them.

Showing one example that those reasons could be wrong in highly selective circumstances doesn't say much here.  There's a select few indie devs that could make a select few IPs work.  But the majority of IP hele by Nintendo?  So few, so very few have the means to handle them.  I mean, just look at your example: Sonic Mania is handled as a partnership with indies but Sonic 2017 is not.  

Also, your definition of indie you put up is just plain false.  Indie means independently developed out from under the auspices and restrictions of a traditional publisher relationship.  You can have 5 developers like Shin'en, or a 100.  You can have a budget of 25,000 like Freedom Planet or millions like Yooka-Laylee.  You can self distribute or find physical distribution after the fact.  This is video games, not books, the definition of indie is different because the relationships between the various sectors of the industry are different.

And Nintendo isn't classified as indie because Nintendo is not a developer, it is a publisher, hardware manufacturer, and parrent company. Nintendo EAD, Monolith Soft, Retro, these are the developers opperating under the umbrella of "Nintendo".  It's no different at all than Bethesda Game Studios' relationship with Bethesda Softworks.  It's not size, it's structure and whether or not the studios are opperating under the auspices and restrictions of a parrent company/publisher/etc.  

I could definitely see a few options that could work out nicely.
Shin'en/F-zero

Yatch Club/2D metroid/Kirby

Playtonic/Diddy kong racing/Donkey kong 64 sequel/ or even 3d mario/mariokart

Stardew Valley dev/A more complex Animal Crossing

Is this even a common practice in the games industry?

I actually look at it on the indie developer side. They always do spiritual successors, because they have complete freedom to do whatever they want. If they were to work with Nintendo or any other big company's IP, they would have to be supervised all the time, meet deadlines, and won't have as much creative freedom.

And when the independent industry is a hit or fail market, I would assume Nintendo wouldn't want to lend their IPs.

Absolutely nobody considers a studio that is 100+ men strong an indie developer. 

Why would they lend out their flagship titles to an unproven indie developer? Lmao. 

Same goes for Animal Crossing, but without the unproven part. 

What people consider a thing is irrelevant, what a thing *is* does not change with the whims of people's arbitrary definitions.  The point of indie as a concept is that one is independent: free of the restrictions imposed by working in the traditional publisher-developer relationship.  Freedom, in other words.  That can be a reality with 10, 20, 30, even a 1000 developers.  The only limitation is how big a team you can assemble and how much in the way of funds you can raise.  Relegating the "indie" concept to rag tag groups of 25 or less working on weird games or retro games is a silly and completely baseless restriction. 

In short, "indie" is not and was never meant to be a "genre" of games. 

There isn't even a canonic definition of indie games.

Size obviously matters because there comes a point where a company becomes big enough to self-publish their games (digitally or at retail). 

https://en.wikipedia.org/wiki/Indie_game

And like I said, no one considers a studio of more than 100 men an indie developer. What's the point of a definition if nobody adheres to it?

Being able to self publish as a developer is not the dividing line, that's ridiculous.  In the digital age nearly anyone can self publish.  You can self publish with five people or fewer.

And Indie - that is Independent Developer - is a term that, on its face, has a matter-of-fact denotative meaning.  It's hardly a matter of debate.

And Wikipedia - by its very  nature - is not the most credible source. 

I love you for this

Ask Games Workshop what happens when you let people use your licenses.