There is no way Vader would stand a chance against the Emperor in his prime. The most powerful psychic being in the Universe vs a Sith apprentice whose master cannot wait to replace is hardly any contest. However, in the Emperor's "current" state of being interred in the Golden Throne it is a much more interesting contest. Vader would be stronger in the physical realm, so the question is whether the Emperor has enough power or even the ability to mount an effective defense of himself. Assuming Vader can overcome the Adeptus Custodes (very unlikely), I doubt the Emperor would stand a chance, especially when someone like Cypher is supposed to be able to kill him. I would not discount the Emperor straight up destroying Vader's mind though.