So, you're comparing your iPhone 5s which is on a jailbroken iOS 8.4 to your new iPhone 6s, which is on the stock, non-jailbroken version of iOS 9.0, and there's a storage discrepancy between the two devices? With the 6s having less available storage? Just putting this out there as a theory but maybe the fact that you're on two DIFFERENT versions of iOS - with one of them being an older, jailbroken release MIGHT have something to do with this variation in available storage. You're not really comparing Apples to Apples storage wise here (pun intended). Yes, both are 16gb devices, but... they're not on the same version of iOS, as well - one of them is also jailbroken. Maybe your 5s being on a jailbroken iOS 8.4 could be the reason why you have more storage available on it than on your stock iOS 9.0 6s, idk??
I guess if jail breaking IS the reason for this discrepancy, then all I can say for you and your new 6s is to wait/hope for the iOS 9.x jailbreak to happen...