While flipping through the DMG again yesterday, I saw that Toughness is one of the feat prerequisites for Dwarven Defender.
A class aimed at fighters. For a race with Constitution bonus. That has d12 hit dice. And whose main ability gives it a +4 bonus to Constitution.
Also Endurance, for a class whose main ability is to keep standing in place. And that definitely won't be able to swim.
Any time I look at a prestige class, I hate the concept even more.
Prestige classes are an example of emergent game design. As originally pitched in the DMG, a Prestige Class was a unique class that had a special role in the campaign- a member of a mysterious Assassin's Guild, or a Sorcerer who has sacrificed magical power to become a Dragon...the idea of the Prestige Class was to give players a path to become such a unique character. This never meant all Prestige Classes are available in all campaigns- if you look at even ones published later, each has their own unique lore!
Prestige Class design states that there should be special requirements, and these were chosen for conceptual reasons, not mechanical ones, beyond "you should be this level to ride this ride". Not every character was intended to gain a Prestige Class (originally), nor would every character want one.
As the game progressed, however, the idea of using Prestige Classes to be things players would actually want to have, making them "advanced classes" developed- as did the idea of using Prestige Classes to patch weak areas of the rules, like multiclassing. And both kinds of Prestige Classes continued to be printed throughout 3e's history.
Instead of sitting down and redefining Prestige Class requirements to be something sensical, they continued to use the same paradigm- a paradigm that exists with Feats themselves (just look at Combat Expertise, and how it generally has nothing in common with Feats that require it). Maybe they thought changing it would wreak havoc with previous content, I don't know.
That having been said, one of the books did try to offer an option, where instead of needing mechanical requirements, you could replace them with challenges- instead of needing, say, 7 ranks of Basketweaving, the DM could say "one of the tasks you need to do is make a DC 22 Basketweaving check as part of the trial to become an Epic Weaver". This never became popular, since it was only ever mentioned in one book, and to be honest, had it's own problems-
If you have to do something special to get the powers of a Prestige Class, then the possibility of cheesing your way into getting one without any real cost would be dead on arrival at most tables. Not because there's a problem with the system, but because WotC increased the power level of Prestige Classes.
Like, nobody is excited to become a Green Star Adept, which, unless you built your character in a very specific way, might actually be detrimental to them (the example GSA is a Barbarian, who will eventually have no Constitution score...ouch!).
But when the game has stuff like Planar Shepherds as options, yeah, that's something you really need to put tough requirements on.
Compare and contrast Pathfinder 1e, where almost nobody takes a Prestige Class because they're mostly terrible and in many cases are worse than not having one at all...but they continued to make them difficult to qualify for.