For those that have the mindset of I don't use these features I just want my Nintendo console to play games, consider this:
Why folders are a good feature - A buddy and me are going to visit a friend for a three day weekend. I have a decent library of digital games and I can't always remember what games are co-op/local multiplayer, etc. Plus it would be clunky to sift through my entire library. So I can make folders for games that are good for something like three player co-op or local multiplayer and it's easy to go through them with my friends to decide what we feel like playing.
System chat -
First, as nice as smartphone apps might be I don't think we should consider that a viable alternative. Whether a phone is charging away from you, broken, no signal, or you don't have one, it's not good being the only method.
Now, I don't play online games much anymore. When I do it's normally with my friends and we can just text. But what if you are playing something with people you aren't friends with in real life and your headset dies? Or you don't have one. You can send a quick message via the console. In some instances you might take a screenshot and it's easiest and quickest to just send it in a message via the console. Not everybody is going to have a discord channel or another way of communicating with people outside of the system. This is also why a system level voice chat should be a standard feature.
Netflix and other apps -
Being a portable system, a lot of people will take their Switch places where they wouldn't a console. Whether it's on a commute or a trip, having something like the switch is great, but you might not always feel like playing games. I personally can never will get into playing something when I'm riding in a car for example, so you can watch Netflix or something similar. While your phone is certainly an option, the switch has a larger screen so it would be a better viewing experience. And it has a built in stand so there are instances where it's also more convenient than a phone.
Trophies -
Unlike a lot of the other missing features this is the only one where I understand the argument to not have it even if I disagree. However, a trophy system has become pretty ubiquitous so its absence is noticeable. And one example of why it's nice to have them is me and a friend of mine will find a few games a year where we can play together, and it's genuinely fun to work towards getting the platinum together (we call it platinum bros). I remember we worked on Metal Gear Solid Peace Walker for like a year, and he even bought peace walker shirts anticipating us getting the platinum whenever I came to visit him. Without a trophy system, there wouldn't be this secondary reward system that can make playing games that much more fun. We wouldn't have matching shirts or silly nicknames without them.
These are just some examples. The defense of "I don't use that feature" or "I don't see the need" is about as weak an argument as you can make. I have never streamed a game on twitch. I have never watched a game on twitch. There's a good chance both of those will always be true. That doesn't mean a game console in 2019 wouldn't benefit from having this feature I care nothing about...because as much of a surprise as this is to some people others might actually really appreciate these features.