How did it come to this?

I quote from the AD&D Dungeonmaster's Guide, page 20, the rules for creating new character classes:

"[A] factor to consider...is whether a new class is really needed. Some players want to create a class for every profession or ability--jesters, witches, vampire hunters, mountaineers, etc. They forget that these are really roles, not classes.
What is a viking but a fighter with a certain outlook on life and warfare? A witch is really nothing but a female wizard. A vampire hunter is only a title assumed by a character of any class who is dedicated to the destruction and elmination of those loathsome creatures...
Before creating a character class, stop and ask yourself, "Is there already a character class that can fill the niche?" Think of ways an existing class could fulfill the desired goal through role-playing and careful choice of proficiencies. A mountainer could easily be a fighter or anger born and bred in hte mountains...[c]learly there is no need for a mountaineer class."

A quick look at the number of "base" classes in 3.5 reveals upwards of 60, perhaps more than 70. The veteran player can only respond with a hearty "what the hell?"
The sad fact is, most if not all of those base classes are covered by applying a concept to one of the core classes. As I see it, all you need are the 11 old standbys, the psionic classes (if you choose to use psionics, which will be another post) and the artificer. Perhaps one or two of the others, but I'm not buying that idea cheap. Most, if not all of these classes, violate the exact statements I quoted above; don't make a class for every role or title.
Let's take a look at a few; witch, ninja, samurai, warmage, dread necromancer, swashbuckler, spellthief. What is a witch but a female wizard, or sorceror, or for that matter, a druid, or a druid/sorceress or druid/wizard? A ninja is a rogue who goes nuts with the Hide/Move Silently and picks up some Craft: Alchemy. A samurai is a fighter (or, for that matter, a paladin or ranger or monk or any combination of the above) who is Lawful, and sworn to a lord/code of behavior; a great example of this (well, ok, not so great, but still) is Miko from the Order of the Stick webcomic. She's a monk/paladin but goes by the title "Samurai." No need for a class, nor even the prestige class.
Continuing the trend; what's a warmage but a wizard who specializes in useful battlefield spells? A "dread necromancer" is a bit of a fancy title for a freakin' base class, init?
"Oh, you're a dread necromancer, are you?" says Joe the 1st level fighter, sneering.
"Why yes, yes I guuuuhrk," says Jalortho the now dead dread necromancer, realizing with his last thought that "dread" should be a title only applied to people who've freakin' earned it, which excludes all 1st level chumps. Meanwhile, Joe cleans his sword and rifles Jalortho's pockets.
A swashbuckler is a rogue, or bard, or pirate, or fighter, or ranger, who arranges his skills, fighting style, background, and attitude a certain way. That's all. It doesn't need a class.
And don't get me started on the variant paladins. That's a whole other can of worms I will address in time. Suffice to say, Paladins are lawful good, period, end of story. I will explain why they should be another time.

EDIT:
I realize that 3.x is a new edition of the game, and many years removed from the quote I opened this post with. But I don't think that changes anything. The point is still valid; 3.x keeps violating some of the best principles of AD&D. Now, don't get me wrong; 3.x is a better system. I don't deny that. I don't see why the principles behind things couldn't have been the same, but they aren't. It used to be, "If you don't like a rule, or have trouble interpreting it, or want to change it, go ahead." The Golden Rule was: there are no rules. Now, if you have trouble understanding a rule, you go read "Ask the Sage" or any of the online FAQS, and if you ignore the Sage's advice (most of which I think is egregiously stupid, especially in regards to PrCs, but I'll address that later) then you draw the wrath of rules lawyers! Which is why I don't want rules lawyers at my table. I said it before, I'll say it again; Skip Williams isn't going to come to your table to audit you and then decide to take your books away.