PWT considers legendary Pokemon as Ubers/too powerful and hence doesn't allow them in.
Within legendaries themselves there are huge power-drifts. Eg- The musketeer foursome (terrakion, virizion, cobalion, keldeo) are allowed in PWT as their base stat total (BST) doesn't exceed 600. But devastation incarnates like Kyurem-W which have BST of 700 would just make PWT too easy, hence they are not allowed.
Latias and Latios are considered to be one of the moderate legendaries and so, PWT accepts them in.