What would be wrong with using a 48MHz oscillator instead of the 16MHz one? They’re a similar price and draw the same current. DSC6003JI2A-048.0000-ND $0.96/1 DK
If this were the default, people who wanted to use USB or just use 48MHz as a clock frequency would be happy, but in addition people could use the single available PLL to make another frequency. Slower or faster.
There would be no impediment to using USB in all designs.