What is the lamest prestige class concept (to you)

[Rubik]

You're missing the point. Its a fluff reason. It is purely a fluff reason. But the fluff in the books is all they had to work with. And until you can understand that the fluff was actually an important factor to some of these classes, you will not understand the point.

If I want my character to be something else, fluff-wise, but use the same mechanics, default fluff is utterly irrelevant.

Plus, my human character (using his racial feat to attain a sorcerer bloodline based on illusion) is WAY MORE magical than your gnome. But he still can't take shadowcraft mage.

Because gnomes, while magical, are illusionists/pranksters. That fits the bard archetype better than Wizard. Elves have Wizard as their favored class because they are, as a people, more focused and more importantly, old. They are independent and likely to put the time and effort into the study of the arcane. Gnomes, while long lived, are much more flighty in their pursuits. But if they do put the time and effort into the study, it will likely be into ways to expand their innate talents. Humans have Any as their favored class because they are mutable and able to quickly learn new things(also why they alone qualify for Able Learner and Chameleon)

None of which prevents my human from being even better at being a shadowcraft mage than your gnome, or my transmuter warforged from being a better chameleon than your human.

Mechanics- OR fluff-wise.

Rubik, we're going to disagree. That's just it. But you need to open your eyes to more than just the mechanics of the game and look at the fluff that accompanies the classes and races in the books that define this game. Until you can do so you will not truly understand the game.

Au contraire. You need to open your eyes to the possibilities beyond default fluff. Otherwise, you're stuck seeing the fighter as the "best fighting class" (which it isn't), the monk as "the ultimate martial artist" (which it isn't), and gnomes as "the best shadowcraft mages" (which they aren't).

The writers of the books were trying to build a world and craft a story without saying "here's our world. play in it." they left it vague enough that it could be modified, but defined enough to that options were unique. Without uniqueness it is a poor story.

It's not the writers who build the DM's world. It's the DM who builds his world. And its the players who craft the story.

If there's no legitimate mechanical reason for a restriction to be in place, it shouldn't be there. A writer telling me what kinds of characters I'm allowed to play when he's not involved at my table is just ridiculous.

Keep in mind that gnomes had a special connection with illussions since 1st edition of the game. If 3.5 stayed the way 3.0 was (with Illusionist being the favoured class for the gnome) would you still argue that there is no connection there and there should be no racial requirement for the Shadowcraft mage?

Yes. Because my human can be a better illusionist than a 3.0 gnome, if I use my feat to do so. Pointless restrictions are pointless.