Does anyone know games that are similar to this in having transformation abilities that allow access to unexplored parts of an interconnected world? Except Metroid and Castlevania :)
The first game that comes to me is Legacy of Kain: Soul Reaver, but it's 3D and you probably already know it.
Ironically I'll have to say New Super Mario Bros for the DS. If you had either the giant mushroom or the shrink mushroom at the end of certain stages, you would get to previously unavailable ones by either smashing through some big obstacle, or fitting in a tiny hole and sneaking under the normal exit. So... not the obvious pick, but it somewhat fits what you're saying to a degree. ;)