They are both pretty much same. X6 was designed from get-go to have a M badge and M division was involved in the initial design of X6. X5 M on other hand is an afterthought. BMW did not intend to bring the M version of X5 during design stages. It was the chief of Spartanburg plant moved over to be chief of M division, who decided, combined with the fact that R&D will be split on 2 models.

Having said that X6 M should have marginally better overall performance and handling than X5 M. Also the reason why BMW gave the media X6 M as test drive car rather than X5 M.