The obvious difference is Android vs. iOS -- both have advantages and disadvantages, most of which you may be aware of.
Both have very fast fingerprint sensors; from what I've seen, the 6s may be slightly faster, the 6Ps seems to be more accurate and learns new fingers much faster. Both work so fast that some people complain that notifications on the lock screen are almost impossible to read.
Both seem to be solidly made, assembled in China -- and the 6s Plus is almost exactly the same size physically as the 6P.
Cameras are quite good in both. The Nexus seems to have a hardware advantage, the 6P seems to have a slightly better camera module, the 6s seems to have a better camera app.
I suppose it is also worth mentioning that, at least without subsidy, the iPhone 6s Plus costs $250 more than the $500 Nexus 6P.
Both appear to be the best phones of their OS, with fans of both sides claiming theirs is better. Which you should use seems to largely depend on if you prefer iOS or Android, or if there is a feature of either you want/need.