I'll bet the ubiquitous "penny cup" at most cash registers is the culprit.
With the "penny cup", very few transactions end up requiring multiple pennies and an associated nickel in change. If the clerk rings up $.91 and you throw down a dollar, and you don't have a penny, the "penny cup" will produce a dime in change rather than four pennies and a nickel.
I believe you're right. Penny cups have become so ubiquitous that I find myself very annoyed when dealing with an establishment that fails to follow the practice.
These new designer nickels, however, are annoying in themselves. Without looking at them closely I keep misidentifying them as the state quarters.
One more thing - most other countries follow a scheme where their coins increase in size along with their denominations. I've always wondered why our pennies and nickels are larger than dimes.