1. All those Ubuntu flavors are for users from Windows who can’t do something like “apt-get install xfce4”. They’re mainly for OOTB experience, and in that sense you have a point that it’s stupid.
2. One of the main reasons is because Debian picked systemd, so other systems that are based off it, like Ubuntu and Mint, decided to follow. Canonical just went along with Debian (http://www.markshuttleworth.com/archives/1316). Luckily, there are still some systems that don’t have it. And not having dependencies is a feature of Slackware.
3. I disagree with your argument, because I think modularity is good. The main advantage I see to having a base system is that you don’t have different ABIs and thus it’s easier for companies to write proprietary software. But modularity means you can pick and choose the best parts. For example, GNU grep is 10x faster than BSD grep. Of course people switch it out for GNU grep anyways, but this is sort of what you get with a base system.
Note that’s not my reddit account making those comments. However I do agree with him.
But I guess really, what I have to say in response to your article is, to each their own. Also, Void, Gentoo, Alpine, etc. would solve the first 2 problems. The 3rd problem won’t be solved, because this is what happens when you only have a kernel and call that Linux.