Since he is going to play an Assassin, he will have stealth. I would recommend going with the Agent and becoming an Operative so you can have stealth too. That way you can sneak past any NPCs that you don't want to have to bother with. (And dual stealthers are fun in a warzone. Nothing says "Surprise!" like two guys jumping out of the shadows at you.)
As far as story is concerned, you can't go wrong with either the Agent or the Warrior. And you can always switch back to your Powertech once he reaches level 24 if you don't like the class that you picked to level with him.
Pretty much what I woud say and sith isnt a great story to me its all kill this kill that but some parts like end of act 1 and 3 are really epic feeling agent on the other hand has the ultimate story.