First, Nintendo was going through an arrogant phase in the last few years of the Wii. This lead to games like Mario Galaxy 2 (complete with a DVD telling you how to jump and insulting your intelligence), Metroid Other M, and Skyward Sword (a game about puzzles). The latter is interesting because there was already a Zelda game on the system that sold much better.
Nintendo wanted to make the games they wanted, not the games the market wanted. So Nintendo thought if they use the Wii branding and make their games, they would sell just like Wii Sports, Mario Kart and New Super Mario Bros. This is how 3D Mario became a copy of 2D Mario complete with powerups and a goal flag. Nintendo made Pikmin 3 because Miyamoto wanted Pikmin to be successful. The games and the system were serving Nintendo developers. There was even Wind Waker HD, Aonuma's baby but now with the Wii branding (I should also note the 3DS had a lot of the same problems which promted Nintendo to slash the price. It was games like Mario Kart, Animal Crossing and Pokemon that saved that system).
There was also a lot of disjoint in the library. Nintendo wanted more "mature" games, so they got tons of AAA ports (which is why I gawk when analyst suggest the Switch needs more AAA games. It didn't help the Wii U). Nintendo launched the system with gritty Zombie U but had sugar coated candy land Nintendo Land. You have mature Bayonetta going nude to attack and then DA DA DA Captain Toad's Treasure Tracker. Who was this system appealing too. BTW, Nintendo Land is an another games that hurt the system. Wii Sports wasn't a minigame collection but was a sports compilation. Consumers didn't see it as a collection of small games but a collection of sports games. This is why Nintendo Land never took off. Minigame collections aren't that hot.
Lastly, the Gamepad was never going to work. Look at what Nintendo came up with. Very few of the ideas were actually that great. For example, Star Fox Zero had gryo controls which helped to improve the game, but then you had this gamepad that you had to focus on and you normally wouldn't use it unless you were fighting Star Wolf. In fact, the gamepad took away from that game. The only games that used it well were Splatoon, Mario Maker, and Star Fox Guard. The former is getting a sequel and all they are doing is changing how the map works. So even though Splatoon used it, it wasn't that crucial. Its also clear Breath of the Wild was going to use the gamepad, but was quickly dropped and it doesn't effect the game in the slightest. Nintendo misunderstood why people liked motion controls. Motion controls added to games and made them feel real to the average consumer. Nintendo saw this as "OHHHH, people like integrated hardware/software," and made the gamepad. No one liked the gamepad and Nintendo could never make a breakout hit with it
So, to sum it all up, the issue was the games. Why is the Switch so successful. Because Breath of the Wild is that good. Good games sell systems while bad games don't. Nintendo made bad games that they wanted to make, and the end result was the system flopped. They thought that if they had the Wii branding, everything would be fine. The reality is that consumers are smarter than that.
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