Why Does Pay-Per-Last-N-Shares (PPLNS) Often Have Lower Fees than PPS?
PPLNS fees are lower because the risk of variance is shifted from the pool operator back to the miners. PPLNS only pays out based on the number of shares submitted in the last 'N' rounds when a block is found.
Since the operator is not guaranteeing a payout for every share submitted, their risk is lower, allowing them to charge a smaller percentage fee.