I find it amazing that a game that worries so much about balance--as D&D has since 3e--can't figure out a way to make a CR system (or some other measure of "encounter balance") worth a shit. Sure, not everyone would use such a system even if it were flawless, but I'd rather not have a greatly flawed system that many do try to use fucking up a game.
It's because the newer versions of D&D have almost no balance. They can't. As the number of "fiddly bits" in character abilities, powers, spells, etc., increase, the ability to "balance" the game (i.e. have similar outcomes across varied characters) grows more and more difficult. The more character "choices," the more that unexpected synergies crop up.
It's also the reason that people who complain that the game was less balanced in the early editions are objectively wrong (at least with respect to combat efficiency). While fighters and magic-users definitely had different power curves, there were no "builds" to create synergies (the best you could do is find complimentary magic items). It was far easier to have a consistent play experience (combat-wise) in AD&D than in 5e, so "CR" was unneeded (HD worked well enough).
This is why 5e's CR system is hot garbage. First, it cannot take into account monster's own ability synergies; second, it cannot factor in the action economy. Third, it cannot account for PC builds or variable effectiveness. At most, it is a simple reflection of a monster's HP, to hit, and damage potential per round. And, honestly, you'd be better off just listing monsters by those qualities than trying to create a system that can design the "proper" number of encounters per day via "experience budgets," etc.
And all this is only a problem if you subscribe to the very modern notion that every encounter (combat or no) should be scaled so that it is winnable by the party (survivable is different). Some of my party's very best experiences have been fighting retreats while they are getting mauled, setting up a revenge fight several levels later. It's why I lament that 5e's random encounter tables are by CR first, and not by environment. If you're on the plains of the Serengeti, you don't get to not encounter a lion just because you aren't prepared to face one...