It does seem pretty strange that the Shichibukai system existed for around 20 years to counter only 3 Emperors for most of that time. The Gorosei did not tell us the balance was designed for a Sanko that only recently became a Yonko, but it's possible.
There might have been a 4th emperor that was defeated/killed and Shanks was either responsible or merely filled in their place several years after the fact. We do have Silver Axe, Ouchouko, etc. as new big names to play around with.
If Oda is still giving Roger and Garp incredible battles, as if they weren't legendary enough, maybe when Shanks enters the story we'll learn that he earned his 4 billion by taking out an Emperor 6 years ago