I always thought that was poor design.
My suspicion is that a lot of the 3.X designers would agree with you. Looking back on certain things that they changed over the life of the edition, it really gave off the same vibe as when a computer operating system gets patches released: people think "why didn't they fix these problems
before the product was released?" not realizing that the product is so large and with so many interacting components that it's almost impossible to do that, even with playtesting.
For instance, I can't remember where I read this, but I recall reading someone talking about how the presumption was that sorcerers, with their ability to decide on-the-fly what spells they were going to cast, were a much stronger class than wizards (even with a limited set of spells known). That was why they made their spell progression lag one level behind wizards (and made it so sorcerers using metamagic had to use a full-round action, which locked them out of Quicken Spell). In fact, that turned out very much not to be the case, since sorcerers were the ones who took a hit to their overall utility via the "spells known" limit.
Or how they didn't realize that paladin spellcasting was so drastically limited by making it Wisdom-dependent, when paladins already needed Strength and Constitution to be a front-line combatant, and used Charisma for several of their special abilities.
Complete Champion's Battle Blessing feat (which made all paladin spells be cast as swift actions if their normal casting time was a standard action, or be a standard action if their normal casting time was a full-round action or longer, all for no spell level adjustment) was clearly an attempt to make paladin spellcasting at least a little better without rewriting too much.
Or the
late-stage removal of
polymorph among monsters that had it in favor of the "change shape" special quality.
It's easy to forget that a lot of 3.X's design was made blindly (for lack of a better word) with the full realization of how it actually worked in play only becoming clear years later.