Given everything we've seen and heard, I think its going to be the software overlap and symbiosis between handheld and console and mobile. An "expansive and continuous software environment" so to speak.
The PS4/Vita cross-buy/play taken further and expanded upon.
I don't think Gen 1 NX will have time or the luxury of introducing expensive hardware hooks, or trying to reinvent the wheel on software delivery.
This. Iwata expressed three concerns last year about Nintendo's current way of doing things:
1) The cyclical nature of a console generation means the tide can easily turn in favour of a competitor or different platform holder when a new generation rolls around.
2) Every new generation begins with an effective software library of zero, making it very risky to launch brand new hardware
3) Software shortages when Nintendo and other developers try to juggle developing for 3DS and Wii U. It's one or the other, one tends to cannibalise the other too.
Based on comments from Iwata from both this year and last, the NX platform is aimed at tackling these issues by giving developers a way program for all NX hardware at once -- Iwata cited iOS and the iPhone/iPad/iPod Touch as examples. That solves 3) as developers can target either an NX handheld or NX console or larger iPad like NX handheld or whatever the form factors are, and optimise quickly and cheaply for each configuration. Like you mention, it also makes "cross-buy" work for more widely like it does on iOS and Android. By making it low-cost to target each system, cross-buy can become prevalent and sustainable across the entire platform, not just for independent games and the odd first party offering.
This will be a scalable platform that will retain its software library over generations, much like iOS software or PC software does (Valve is in a position to benefit from that). That solves problems 1 and 2. Indeed, Valve is exposed to little risk at the moment, having built up an extensive library of software and contracts in the long term. Any new competitor hoping to do battle with them in the PC space will need to start from zero, much like Microsoft will be with the Windows 10 storefront.
Nintendo's thus exposed to less risk the longer the platform keeps going for. In the short-term, 3DS, Wii U and Amiibo for those platforms shields them from risk. In the long term, even if NX has a tiny software library at launch, the platform will continue to develop and evolve over time that there will be a point at which it eventually becomes "good enough".
Nintendo can also release new hardware or form factors without having to start from scratch; they can fend off competitors much more easily as well. If Sony actually does end up making another handheld, Nintendo can release a "New NX handheld" while still allowing developers to maintain compatibility with the older handheld.
This is doable in the long run. iOS Devices from 2011 with the Apple A5 SoC still receive regular updates from Apple and support from developers, and they are approaching 5 years old now. The iPad 2 launched on the same day as the 3DS in some countries -- by the time developers and Apple stop supporting it it'll be at least as long as a standard console generation. Furthermore, the iPod Touch has been cannibalised sales-wise by the iPad, yet developing across all the various iOS hardware configurations is low-cost enough that Apple can continue supporting it, and developers continue to targeting it with their software.
So Iwata's comments about not knowing whether only one device may be needed in the future suggests Nintendo will test the waters with several form factors at first, and is unafraid to let one rule over the other. For example, an NX Handheld XL with a higher screen resolution and more real estate that developers can actually use (versus the 3DS XL which developers cannot target specifically) might cannibalise NX Handheld sales. It won't be the end for anyone buying or supporting the original NX Handheld though, and Nintendo would have been able to take the platform in a new direction with the theoretical NX Handheld XL.
Nintendo just needs to make sure the first set of hardware is future proof so they can ensure developers are able to support it for a long period of time. That way they can release new form factors and hardware without peeving off owners of early gen hardware who might not upgrade immediately. They should also encourage developers to adopt a "bottom-up" approach for some of their games, so that they still work great on older hardware before its lifecycle is up. That goes hand in hand with ensuring the first set of NX hardware is futureproof at the time when it launches.
Investing in DeNA for services and to build a new cloud based platform is smart -- Nintendo will likely want things to be as seamless as possible when switching between hardware on the NX platform.