In "Dark Lord" Palpatine was on the opinion that Vader blocks were psychological ones, so he had go get the guy out his depression "at his own risk". In "Shadows of Empire" Vader managed to temporarily heal his own lungs and breath unaided for minutes, so yes, a Vader that truly and fully embraced the Dark Side would mop the floor with the Emperor.
Remember how Jacen managed to achieve an state of unity with the Force to the point of glowing, how Krayt managed to learn Cade technique and return from the dead, so Vader who was leagues ahead of them fully immersed in the Dark Side would like a walking Force Nexus.