(This ended up being longer than I expected so I went back and bolded the key points for skimming purposes.)
If you read around the internet (and not just Neogaf though forum members there have been good about culling rumors and quotes from Nintendo, and putting the tech stuff in context), I think there's enough to formulate a reasonable conclusion. There will be a console and a handheld. Reading over Iwata's interviews over the past few years, a shared library seemed like an obvious verdict. Once I started lurking Neogaf more frequently, I noticed the idea was gaining traction. I doubt I'm the first one to think of it, but I felt a little vindicated that others were arriving at the same conclusion.
The library will NOT be 100% shared because third parties will decide which of their games will and will not play on both though Japanese third parties that released successful 3DS software will likely have their games shared if only because it makes more sense to do so. It allows them to sell to a wider audience. Very rarely will we see PC/console games scaled down since that may affect the integrity of the product.
More often than not, first party games will be shared. If a game is too intensive for a handheld (probably anything Monolith Soft pitches), Nintendo will likely greenlight a console exclusive because it's been very good lately about not compromising a creator's vision (e.g. Bayonetta 2). I'm sure some are going to complain about Nintendo holding its first party output back by making games compatible on weaker handheld hardware, but those people are silly and they don't know what they're talking about. Nintendo has been making console-level games on handhelds for at least a generation. It has always valued gameplay over graphics. More to the point, it has always valued art direction and design over graphics. As Nintendo transitions to more powerful handheld hardware, the only difference in terms of its handheld and console output will be resolution. A shared library makes more sense now than ever.
Nintendo is abandoning optical media as it's no longer a viable storage solution for video games. The sheer amount of data of most modern games cannot be read fast enough from an optical disc to display on a screen. This solves a couple of issues. No disc drive cuts cost and no discs mean no installations. Shared library games can be scaled up, but a better solution would be to have the higher resolution textures on the game card and the hardware detects which to display. 540p scales to 1080p easier so expect the handheld screen(s) to be 540p. I suspect digital versions will simply include the texture pack you need depending on the hardware you're playing on. No need to have the larger, higher resolution textures on the handheld.
Nintendo would prefer people buy both console and handheld, but it's a software company first. The point of a shared library is to alleviate droughts and to ultimately release a greater volume of software. Nintendo's thinking is possibly that console owners will have access to all games, but handheld owners will have access to more games than they have before. If a console exclusive game is so desired that a handheld owner buys the console, that's just a win for Nintendo.
Since Nintendo is moving to game cards across the board, physical backwards compatibility is out of the questions, and I doubt Nintendo will bother with an external disc drive. People can still keep their Wii U and Wii, and they'll get over it in time anyway. Still, I expect Nintendo to strive for Virtual Console to include every past generation including Wii U, and be playable on the handheld. Speaking of, for Virtual Console purposes, I fully expect a rebranded Remote/Nunchuk. For simplicity's sake, I think NX's have the standard two sticks, four face buttons, four shoulder buttons, D-Pad, and start/select/home. I'm undecided if the console's main controller includes a screen, but a screen controller is definitely returning.
As far as hardware, specs are not the same as performance, and without proper context, it's hard to tell what Emily Rogers' source means. Still, I expect the console to be in the ballpark of Xbox One and PS4. Unless there's a noticeable jump in performance (which there likely will not be consider NX will not be sold at a launch and releasing over $300 is practically marching it out to die), it doesn't matter if NX is more powerful than PS4. As long as games can be ported, it's ultimately just a business decision whether NX gets support. I expect the handheld to have better performance than Wii U which won't be very difficult in 2017, and only displaying in native 540p would allow the hardware to allocate its power to other things.
I think it's in Nintendo's best interest in the long-run to transition to ARM on the console now, but x86-64 is still a very reasonable expectation. Most modern engines support ARM. The proprietary engines of a few major third party games currently do not. Compiling code for those engines probably isn't especially difficult though it is an extra step. However, the chances of Nintendo getting those games at/around launch or even ever were not very high to begin with. Since regaining support is going to be a long process, this isn't something Nintendo needs to concern itself with right now. And with ARM gaining more and more traction, those proprietary engines or their successors may eventually support ARM. Right now, Nintendo seems to be making all the right moves to create the anti-Wii U. If it has learned anything, I hope it learned that there are no quick fixes, no shortcuts. To improve its market position, Nintendo has to work with what it already has (excellent first party output and key third party output on its handheld) and build from there.
One bit I'm really looking forward to is where My Nintendo fits into puzzle. Right now, it's only compatible with Miitomo (which is weirdly addicting). Players are given "Missions" and completing them Platinum Coins which can be exchanged for discounts or even games. I doubt Nintendo opens up "Missions" to non-mobile games until NX.