I'm a little late but whatever.
These Pokemon do not have the same base stats...
Nor do Shaymin and Shaymin-S have the same viable moves to work with due to, as what chaos stated above, stats and ability too.
I can't really comment on the Ubers (Giratina forms) as I haven't touched Ubers in many months.
On the Rotom forms, the newer variants are almost exactly the same, and the only thing that really differentiates each form are the new moves it gets. All other features of the new forms are the same (obviously not including physical things, like appearance), thus they should be looked at as the same Pokemon.
The normal Rotom should be kept in UU as a different Pokemon due to the different base stats from its Pt forms (despite being used quite similar nowadays to its OU brothers - restalk and occasional WoW).
Option 2 for me .