No, I'm not sure, I am merely speculating based on Fatal Frame 5, another niche Japanese Wii U exclusive.

This.

One of the worst things about Nintendo's output this generation is that instead of giving us the actual games we want, they give us watered spin-offs/minigames as if they think that will shut us up.

"Oh, you want Metroid? Here's some throwaway side story where you play as a Chibi Federation grunt. Oh, and here's another 2D Donkey Kong platformer."

"Oh, you want Zelda? Have a million cameos, spin-offs and remasters while we delay the real thing indefinitely."

"Oh, you want Animal Crossing? Here's  a C-grade Mario party knockoff with Animal Crossing window dressing."

This

they were treated as games. They were given release times with other retail games. No major company, much less Nintendo, publicly announced this much for a concept work/mini game. We can only assume that Nintendo actually meant to release them as games and they either got delayed or cancelled

Saying SMT X FE was cancelled is just wow...
Nintendo didn't even develop it and it'll get more sales from the west than Japan...

Just because a game is not the sequel people want, doesn't automatically make it crap. Would I have prefered a 'true' Metroid sequel? Yes. Doesn't mean I have to hate Federation Force. Also, first you agree with saying you want to get 'sequels to things people want' and then you follow up by complaining you get 'another 2D Donkey Kong platformer'. Ironic because that actually is a pretty good example of a sequel to something people want. Donkey Kong is a big and popular franchise and the games are well received. 

I'm not saying AC amiibo festival isn't a terrible game, or that I wouldn't have liked to see Zelda U by now. If you disagree with the policy of Nintendo, that's fine I'm not arguing on that. However, it seems most people just take it out on Federation Force. Of course you can dislike a game for what it is, if you think it looks bad. But mostly the hate seems to focus on that it is  not Metroid Prime 4, rather than the game itself. 

I think they mentioned both project game in some document a couple of months ago. We will see them before E3 this year

Tropical Freeze was not what most gamers wanted from Retro on Wii U, as evidenced by the widespread disappointment when it was revealed.

As for Federation Force, I think people are well within their rights to be annoyed that it's using the Metroid Prime name to sell what looks like a thoroughly mediocre game with none of the hallmarks of the Trilogy it is named after.

I hope so. Those games looked like ass.

Genei Ibon Roku bombed hard in Japan - no... definite day one buy for me. and I think Metroid Federation Force would still be released.

I don't think this disapointment was as widespread as you claim, more an example of a very vocal fanbase. I could also point to the many people on the internet who claim Tropical Freeze is one of their favorite Wii U games. Besides, Donkey Kong is a much more popular franchise than Metroid. Despite the very small userbase of the Wii U Tropical Freeze has outsold Prime 2. When you include digital sales it will have outsold Other M and is on it's way to outsell Super Metroid. I think it has pretty decent legs so it can climb pretty close to Prime 3 as well.

Also, of course people have the right to be annoyed, I never claimed they don't.  If you think it's a mediocre game that's fine by me. All I'm saying is that I think a lot of people are not prepared to judge federation Force on it's own merits (whether it has any is subjective and besides the point), rather than what it represents.