- Directional Pad (NES)
- Shoulder buttons on controller (SNES)
- third handle on a controller and controllers with expansion slots (N64)
- portable gaming systems (starting with gameboy, which didn't even have a backlit screen)
- subsequent iterations that included: folding designs (SP), Touch screens for interactivity (DS), game sharing (DS), 3D (3DS, designed before 3D was "a thing")
- RFID out-of-game experiences (Amiibos)
- Innovative nunchuck design where moving the controller is an axis of control (Wii)
- A second-screen experience (Wii U)
- ... and these are just the recent/well known innovations. I'm sure I'm missing many (link cable, anyone?)
So, basically, Nintendo has always tried to push the envelope with their consoles. Nintendo isn't interested in making a boring "not-a-pc-i-swear" console.
Nintendo hasn't lost sight of what made them great. In fact, I'd argue that they're still very much on that path. The day we see uninteresting hardware is the day Nintendo has strayed from what made them great.
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.
If the gimmicks that "muck up the same handheld" aren't worth anything, then the vita should have captured a large segment since it had virtually no gimmicks and just solid hardware. Not the case.
Nintendo's portables have added a lot. Please don't tell me that juice is "essentially just water with some flavor gimmicks." yes, everyone is iterating. No, nobody knows what will ultimately pan out and what won't. If you want Mario on PS then say so, but Nintendo is genuinely trying to innovate and think differently. Move and Kinnect are gimmicks. Nintendo will happily devote a generation to do something interesting.
The day Nintendo gives that up and makes an x86 platform running expensive hardware with no "gimmicks" is the day they become a primarily a software developer.
Their portable Game and Watch series included buttons in the direction pad format and even a few folding duel screen models as early as 1982.
Instead, it's a glorified 3DS. =P
Most of all, they made a profit per unit sale of the Wii, when the standard at the time was (is?) to sell consoles at a loss and make it up on fees and sales of games. They made profit on the base Wii, then they profited from all of the other shit they made up to sell for it. When the time came to move on from that gold mine to something new, they predictably tried to strike gold a second time.
They didn't.
Now they're trying a third time, and I suspect it will end badly for them. They've increasingly lost sight of what made them great, blinded by the allure of unbelievably quick and vast quantities of hard cash.