Is not always about been the definitive first, but the first one to do something meaningful with an idea, concept or design. For example, the Tiger.com had a touch screen way before the DS, yet it was so limited in practice that it couldn't exploit the potential for touch screens in game software. On the other hand look how far the applications in gaming for a touch screen soared with the DS, even considering it was quiet limited on itself in comparison to what we have these days.
you basically pointed out features related to gamepad, N64 was out of its time already on June 1996 (ask Squaresoft for details)
This is basically a non answer. Also you didn't respond to things like the SNES shoulder buttons, the N64 triggers and expansion slot which were very atypical at the time of it's release and latter became standards.
Anyway expansion port was probably introduced by Megadrive, multiple holding positions by Atari Lynx, and both in the 80's, not in the middle of 90's
An expansion port in the bottom of the controller? i don't recal the Mega having one. The N64 pad had that modular expansion slot that was used for different accesories such as memory cards, haptic feedback, Gameboy communication and even a screen was planned at some stage.
Also regarding the holding position of the N64 controller. The Trident design is quite unique, specially the centered handle, as it allows the user to confortably hold the entire controller in one hand. That's why i think there's potential still for a design of such characteristics if NIntendo opts to use a touch screen in a pad again. Even Some games supported this feature for stuff like allowing dual analog play or even one handed play.
For me innovative systems are Famicom, PC-Engine, Megadrive, PS1, DC and Xbox. I would add NeoGeo but it was aimed for a too elitarist market
Handheld side, Gameboy, Game Gear and PSP (a multimedia device, you could listen music and watching movies years before Apple products)
I would add PC-Engine GT but it's same as NGAES
i think lumping the PSP in the group shows your bias more than anything. i always liked convergent devices myself too, don't get me wrong and the PSP was quite an astonishing piece of technology at the time, altough not much of an inspired one.
There were accesories for older portable systems such as the Gameboy that allowed to add your handheld extra functionality, stuff like radio or TV tunners, cameras or MP3 players. Not to mention the weird chinese or japanese stuff that is not mainstream.
For some reason you are blocking how out of the ordinary the DS was in it's time. The thing has 2 screens in the first place at a stage where the portable dedicated devices form factors had become quite standard. The book style position you held the system to play something like Brain Training was rather novel for example, even considering earlier things like the Lynx or WonderSwan did in terms of holding positions.