The problem is, 3e is fundamentally broken at its very core, conceptually. The absolute lowest substratum of the
math is functional, in that "d20+mods" is the core of every WotC edition, but once you get higher than that and start looking at the conceptual components, they
badly conflict with one another. Unified saving throws were supposed to make it easier to balance spells; they instead make spells incredibly broken because of how easy it is to jack them into the stratosphere (
without violating any of your assumptions, I should note.) PrCs were supposed to be a fun, flavorful way to add some extra color and to reward creative characters; they instead became horrible mandatory hurdles in order to not fall behind and effectively punished every player who didn't meticulously plan their characters several levels in advance (if not all the way 1-20.) Skill points were supposed to be a fun, semi-naturalistic way of having characters grow and improve dynamically; instead, they punished creative players and anyone who liked melee types except Rogues (but
especially Fighters, Barbarians, and Paladins), while generously rewarding players who planned their characters meticulously and especially full casters who didn't need any more power-ups. Feats were meant to be a huge deal, the major draw of playing a Fighter, something that could truly transform a character...and they ended up being mostly trash used to gatekeep powerful features, with a tiny handful of exceptions that were stupidly, amazingly broken. Iterative attacks were meant to be a simple and powerful way to let melee characters keep up as levels advanced; instead, they punished anyone who wanted to be mobile and enforced a dull and static playstyle on most characters
unless they were spellcasters. Etc., etc.
3e is full of interesting ideas and wonderful aspirations and
absolute garbage implementation. The only way to get an actual, functional game out of the rules is literally to burn it down to the bedrock d20 layer and rebuild the whole thing from scratch. There was no way the CR system could ever hope to be effective or functional, even if they
hadn't gone for the "every monster is built exactly like a PC and thus runs a gamut from Beyond Garbage-Tier to Infinity-Plus-One Powerhouse."
Gotta love needing something to feel like what it literally is because of who made it and what it's labelled as, regardless of what damage that "feel" does to the actual process and experience of
playing it.
Or, wait, no, "love" is the wrong word there, isn't it?