I'm curious mur'phon, what class is your Rep? You said your Rep character is set in stone, but you didn't say which class. That might help cover any redundancies in role. You implied Smuggler, but I wasn't for sure. Actually, your rakghoul infection line probably means it is Smuggler.
Everyone loves the Agent story, and I have an Agent, so I'm going to give a majorly biased vouch for the Agent. Since it's not bound by a movie archetype, it has a lot more freedom in its storytelling, and it has something like 4 different ends to the entire story, influenced by decisions going back to your 30s.
Plus the Agent has one of the craziest band of freaks for companions. No other class can beat the Agent for weird companions. Every class has at least one weird companion, but the Agent has 4(arguably 5) weird companions.
"Sir,we are beginning our search for these rumored 'underwater villages'.They will not stay hidden for long". -Battle Droid Commander OOM-9!