Sure, Prestige Classes introduced in 3.0 were called "optional." They seemed to be a way to specialize your character by replacing levels of Basic Class X with levels of Seemingly Spiffier Prestige Class Y.
And had these PrCs mostly been Tier +0 and few in number, I would be more likely to agree.
I understand WotC is a business out to make a profit. They also didn't understand the scope of their own game. And, PrCs provide obvious specialization without remaking the base classes.
Still, profit motives aside, the glut of PrCs seem to stem from base classes with pretty boring mechanics and levels where the "class features" entry is empty. In all of 3.5, consider how many PrCs there are intended for Druids. Consider how many of them are worth using. Now, consider how many PrCs were meant for Wizards and how many of them we keep hearing about.
I posit then that the designers started waking up to their design flaws. Being an Illusionist was meant to mean you were a Wizard specialized in Illusion. In core, there were no great distinctions between being an Illusionist and being a Transmuter. (Extra spell slots and the forced acquisition of your free Wizard spells by level were the only notable differences.) However, a Transmuter/War Weaver feels a lot different than an Illusionist/Shadowcraft Mage. It isn't just "I focus on casting different spells!" It's "I have synergizing class features that greatly distinguish you from me!"
Tome of Battle base classes were a great step forward in this direction. Gish classes aside, if given the choice, I'm more likely to take a martial adept base class than a ToB PrC. Why? The maneuvers and stances can greatly distinguish Warblade A from Warblade B, and both Warblades have some spiffy class features. (Not enough for me, but at least a good start.)
So, whatchya think on this situation?