I loved the JC. And come on, if saving the infected had actually made the character weaker in mechanics people would have had endless fits.
It's gameplay and story segragation. Live with it.
I thought learning more about the Force and having the totally unique role in the Order was awesome. And I didn't think being a Shadow worked against the story at all. I saw myself as the mysterious Jedi hero who appears from nowhere, saves the day and is gone again.