But a human/elf/dwarf/halfling can take levels in wizard or sorcerer (!) or psion or cleric or druid just as easily as a gnome. "Being very slightly more magical in a very tiny way" doesn't mean you're barred from being magical. If shadowcraft mage actually specifically worked to improve the gnome's racial abilities, I could see your point. But it doesn't, and so I don't.
Then why is the elf's favored class wizard, if gnomes are so much more magical? Why does a human with wizard as his class have wizard as his favored class, if gnomes are so much more magical? Why do gnomes have bard as their favored class, if gnomes are so much more magical?