Anakin wasn't ever totally 'dead'. He was mostly dead, which is different from dead dead (If you've ever seen the movie "Princess Bride" there was a line that goes something like that, which makes sense in this case). Or at least he got 'resurrected'.
So Anakin, not Vader, threw the Emperor down the shaft, and Vader wasn't going to try to assume the Sith mastership.
Yes, in the end it comes down to Lucas overexplaning things and boxing himself in on other things, but something like that might make sense...