I think we can all agree that the major upside to using Steam to play SWTOR is that there is no Bitraider that causes all kinds of bugs and glitches in the game!
The downside is that whenever Steam rarely crashes, you are sent back to the server selection screen and the servers aren't displayed, same if your internet goes out.
Personally, I'm 50/50 when it comes to having to copy most of the files from the stand-alone SWTOR folder to the Steam SWTOR folder when switching launchers, but to each their own I huess.