The Septims
While the Empire in the Third Era was constantly shifting between stability or instability, it had it's fair share of good Emperors. And it's last Emperor, Uriel Septim, was arguably one of the greatest of them all, next to Tiber Septim himself. Also, it was unliekly for any Septim to outlaw the worship of their ancestor. So I personally believe that The Septim dynasty was, in general, better for Cyrodiil.
The Medes.
We only know of two of the Emperors in this dynasty, Titus I and Titus II. But given with what happened to Cyrodiil and it's remaining provinces, It seemed that The Empire was slowly going to Hell from Titus I to Titus II. While the earlier Medes were good tacticiand and manage to reunite The Empire. (As well as made some minor improvements.) They do not seem to be that good of administators.
And another question. Which Dynasty is more popular in Cyrodiil? The Septims or Medes?