You can really divide that list into two distinct eras:
Era 1: Nintendo is the head of the pack in software and hardware, and not afraid to try new things.
-NES
-Gameboy
-SNES
-Partly N64
-DS
Transitional period: Gamecube. At this point it's pretty clear that Sony is bringing things to the table that Nintendo is struggling to match. It's not a bad console, the GC, and it ends up being almost laughably affordable, but it's the slowpoke of the gen.
Era 2: Wii->Present.
-The Wii, as you say a pretty quirky and novel take on interfaces. This is the period when Nintendo makes a huge part of the fortune they're sitting on today, and expands to a truly staggering userbase. Traditional Nintendo fans (i.e. people who want Mario and other key franchises) are happy, new gamers are happy, people who want one console are not.
-WiiU, frankly stunk. It didn't do what anyone really wanted it to do, it wasn't as inexpensive and cheaply fun as the Wii or GC. The WiiU tried to be the Wii, and a mainstream console, and it wasn't.
-3DS. Not a bad thing, but I'm yet to meet anyone who really gives a shit about the 3D. Another gimmick that gets forced into things, but ultimately the portable brand is full of such incredibly good games that it doesn't matter.
-Modern portable: ... Fantastic. It's hard to argue against Nintendo's mastery of this aspect of gaming. Underpowered, still too focused on gimmicks instead of perfecting the core experience.
-Amiibo... brilliant business move, it's hard to argue against how happy it made some people, but it was also a manipulative money-grab. It was a case of Nintendo understanding how to maximize a fad, but it brought nothing of value to games.
-"Second Screen Experience"... again, it was something you could work with, but it mostly got in the way of developers and ended up being underwhelming.
Nintendo has lost sight of doing something simple, extremely well. The Gameboy was great because it was just a portable gaming machine, and it kept on that way until two screens and 3D gimmicks, and multiple iterations of largely the same handheld started to muck it up.
Hardware has made Nintendo rich, but it's the software that made them great. Mario as a concept and a game was much better than the NES platform and interface. The more Nintendo has made money on hardware, the more their software has suffered.