Look, you can take that list and sort it by GB. Of the hundreds of games there, oddly enough, only 32 games are natively above 32 GB. It's not "cherrypicking." And that list is recent as of the end of January 2016. You can't even begin to say that 32 GB isn't big enough right now for the vast majority of games out there. 32 GB is plenty of size for at least the next few years, and by then, depending on demand, there will be larger sizes anyways. And yes, there are huge patches and DLC, but again, there will be a hard drive anyways for that. There are just tons of game sizes and types. Nintendo's current games apparently are pretty small in comparison to many others currently. Why couldn't this much size work for them and help with their shared library idea? (Along with digital too!)
Also, you're making a lot of assumptions about what Nintendo IS going to do. They COULD do whatever they want regarding internal storage. (Or cartridges for that matter! It's all just guessing right now anyways! It's just that they COULD do this, not that they will.) It's their product, they market to whomever they want and where, etc. There was a quote about expanding their markets to untraditional regions and that they would have to tailor their products accordingly. I mean, the internet infrastructure just isn't there for all digital yet and they still need to have a physical solution. There's still no real legitimate reason to push digital only now when ALL video game profits are rising across the board. (At different clips, but that's not the point anyways.) Choice is best and companies still need to let the market dictate where they sell their products. It would be madness to push just digital only for "higher profit margins" and destroy all the extra chances for advertising and showing a product off in Best Buy or Walmart, for example, and those great, extra opportunities to sell products. They can and will coexist as there is no reason for them not too at this stage.
I personally believe they will have an internal HDD, but I think it doesn't have to be insanely large (definitely no more than 500 GB, but it could definitely be smaller), and I still think they can have their power users who actually desire and want to have more storage to go out and get one or use what they already have. If they want to download a bunch of indie titles or try out digital only for their major releases too, sure, get yourself a very large hard drive to do so, and we won't stop you from doing that or make it prohibitive in any way. Your option break down is a great sounding one to me! Makes sense to have those options and provide different models/bundles based on what the user may intend on doing with it anyways!