In my experience, which surely isn't universal, the problem becomes tailoring things to particular parties. What I mean is that as you say the Encounter Building rules don't function well at most levels (and grows worse over time). So as a DM you (or at least I) get used to tailoring challenges as you go based on instinct and experience. Which works great. Even at high levels, this can be done, and after a while it's not that hard to do it.
Except the higher and higher levels the party gets, I suspect the more those instincts and experiences are honed by the particular party and player composition you're working with at your table.
So by the time you're at level 16, what challenges one party bares very little resemblance to what might challenge some other group.
Now, how do you write an adventure that can properly challenge most level 16 groups, if the best way to do it is to tailor it to the particular group? It becomes a pretty tricky task.