See, this strikes me as a bad idea on palpys part. "Hey, im a sith, hes a sith, sith are known for apprentices betraying and killing their masters once they stop getting stronger..... ill make my apprentice supreme commander of the entire galaxy's military. I dont foresee anything bad possibly happening through that." Didnt palpatine betray and kill his OWN master way back in the day? Seems like he might have thought that decision through a bit better.
Of course, another prime trait of Sith is arrogance - the belief that while they bested their master, they won't make the same mistakes and fall to their own apprentice. And Palpatine did a pretty impressive job hindering Vader from being more powerful (primarily in the EU...but that is also where most of Vader's plotting to overthrow his master is too). And I don't remember if it's covered in the movies or not, but wasn't Palpatine disappointed in the massive damage Vader received and his subsequent lower power?
My homebrew - If you use it, please let me know how it goes!