Jack says, "Allow me to get straight to the point. I don’t hate side missions, in some cases I actually love them. Throughout this article I may sound contradicting (if you’ve ever read any of my other articles), just relax and read through to the end, I’ll explain then.
The problem with side missions is that I never find myself going “oh I should really do this side mission”. I’m very much a straight forward type of thinking man who goes for the throat, and doesn’t bother to look around. And I honestly hate that I’m that guy."
Totally agree with your assessment of those games. I like side quests, when they're done in moderation. When a game is 90% side quests, 10% main story, they did it wrong. Especially the flat out lazy stuff that was in Unity and its companion app.
Deus Ex: HR did sidequests best. Devs should take notes.
It's really on a case-by-case basis here. Even the author agrees to this. Which is weird to have a title that says otherwise.
They shouldn't be eliminated from games. They just need to be more interesting than they are. Add some story element to it or something to spice it up.
If your reasoning for eliminating side missions is not because you think they take away from creative direction from the main story, but only because you never feel obligated to do them, well maybe you should just not do the side missions then. I'll take my chances with worst case scenario getting some extra gameplay hours.