You might have a look at my Dynamic Renamer. With it, you can combine a sequence of transformations, which of course you can store as a single preset. It supports various case transformations (-c) and can do your RE replacement (-/).
So in your case, I think the transformation (the New name) would be something like:
-/S(\d{2})e(\d{2})/Series $1 - Episode $2/ -ct