I think that if they do go the padawan-master route, it would be cool to have a plot like this-
After the "training planet" and the first real planet, you get a master to train you.
If you are LS, your master will be ls and you will save the galaxy together. (Or he will die and you will go on to save the galaxy alone and face his killer)
If you are DS, you will eventually become stronger than your ds master and in the end you will destroy him, take on an apprentice of your own (one of your crew members who is force sensitive. You will train them and then confront your master together.) This should mirror the LS "master death" late in the game- on LS you could take on a padawan. Your master's dieing words telling you that you are ready to train another (once again, a FS crew member)
They might also have some sort of neutral master if they want to add a third dimension to play, you're goal will be to bring stability to the core worlds.
You could keep the same planets and cities (with maybe a few alignment specific areas) but have different side quests, different crew members, and several different endings
And with all scenarios, they need a better romance tie-in! Maybe as DS, the force sensitive crew member could be the one you use to challenge your master with and train as an apprentice. Either way, you should have a lot of options.
As DS, since you have a master, it will allow for a more cool and calculating form of DS, like the kind we see in the movies. Less taking candy from small children, more manipulation and power-hungryness.
As LS, having a master will give it a very movie-like feel as well, and will add a little direction without making the game linear.