I'll weigh in on the other side of the discussion then.
First, let me say that classes which marry fluff and crunch to make a distinctive and memorable whole are flipping awesome. When done well, it helps a character be memorable and fun as well.
That said, I think of classes as packages of abilities, which can get them mixed up with feats. Let's take the example of cheesy martial arts films for an example to clarify. If your master teaches you the Five Point Palm Exploding Heart Technique, that's a feat. It's one discrete thing which not everyone with similar training to you has to be able to do. If your master teaches you the Mantis style instead of the Crane style, that's a different PrC because it makes you more focused on single, powerful strikes and ending combat quickly instead of avoiding and negating your opponent's attacks and winning through attrition. Mechanically, this means you gain sneak attack or some other bonus damage instead of evasion and dodge bonuses to AC and such. Different, thematically similar PrCs. (aside: I have no idea if that is a fair analysis of any Mantis style or any Crane style. It's a decent example though.)
There is one downfall to classes having flavor and mechanics linked, which is exemplified by the Spirit Lion Totem barbarian alternate class feature. Pounce is really, really helpful for mobility of melee characters, and far and away the easiest way to get it is via a one level dip in barb. This means, provided one wants to build a melee character who relies on full attacks, the most effective character will have some barbarian in his background. Refluffing exists: you could have hidden ferocity despite your city upbringing, it could be a secret technique taught to you by aesthetics who occasionally flip out and kill people, etc. But mechanically, that dip in barb is very good and not everyone likes refluffing like I do.
As I just shot myself in the foot by explaining, base classes are pretty flexible. Prestige Classes... I had an example earlier about different martial arts styles, which is kind of relevant here. But my deeper concern is choosing PrCs which have flavor for their mechanical merits due to a lack of other options to get such merits. Master of Many Forms is not guilty of this: it is a class about changing shape, and it makes you better at changing shape. For a list of the offenders, consider the X stat to Y thread
. Want to be so tough that weapons don't hurt you? Deepwarden does it, but you have to be a dwarf with a specific kind of goal in life. Want to be so smart that you are hard to hit? Be a Blade Singer (elf), Eternal Blade (elf), Duelist (limits your combat style), factotoum (base class), or a couple of other also niche options. That's an ability that should just be a feat.
I also don't like strict entry requirements precisely because they require you to intend your character to enter the class. That's just a matter of taste though.
I appear to have weighed in on every discussion, rather than just one side of one of them. Such is life.