Regarding the difficulties of calculating percentages in non-base-ten systems - don't forget the bias implied in the name. Percent = per centum = per 100 ==> base ten is presupposed. In a base-12 world if you made it "per 144," it would still be written as one-zero-zero and the computations would be just as easy. Likewise the shifting of a (duo)decimal point would be just as easy and other shortcuts in arithmetic probably even easier, because of the multiple factors of the base.

As [whoever-it-was] said above, whatever you're used to is what's easiest and "natural."