Since Google has launched Nexus phones, it is the first time that the users have choice of t2o flagship phones. In last 2-3 years, there was the choice of only memory storage and color. But now Nexus has given the choice of two phones, so that you can make your decision.
Nexus 6P is larger than Nexus 5X and you will have to spend some extra money to buy it. But at the same time it has much more features than Nexus 5X. The prices of these 2 models varries from country to country. For example you will have to pay $70 in US to buy 32 GB model of these phones and €120 in Europe.
Source: Nexus 5X product page and Nexus 6P product page