Imperial Agent story is for sure the most dramatic and interesting, but my all round favourite is the Sith Warrior story. It's a slow build up from beginning to end, all the while the epicness grows and grows. Every quest you do seems to have massive effects on the planet/galaxy/war. And it matches really nicely after doing Knight.
however I can't recommend enough playing it 'properly' which so few people do. Instead of just picking LS or DS choices to grind points, instead actually role play it. I have 2 warriors: a juggernaut and marauder. I played the Jug fully DS and it was boring as hell after a while. However, the marauder I played mainly LS but with more than enough DS choices. And it was infinitely more fun and interesting. Instead of playing a dumb (and yes DS Sith are nothing BUT dumb) mindless brute, you play a powerful knight and vanguard for the Empire, hero to your people.
Imperial Agent story is utterly amazing too. You get such a different outlook on everything, and you realise that almost everything that happens in the galaxy is down to Intellligence, not the power plays of Jedi/Sith. You see Galaxy from a 'real' perspective, not of the superhuman Jedi/Sith. But a 'normal' citizen. Plus, you're James Bond meets Hitman.
Bounty Hunter is my least favourite class in game. Chapter 1 is okay, after that it is pretty repetitive and dull.
Sith Inquisitor is weird. Chapter 1 and 2 sucked, but chapter 3 was epic on scale of Agent/Warrior which I personally say does make up for it. It's also very 'different'. As an inquisitor, you really don't give a **** about the Empire, the Republic, the galactic war. Pure interested in your personal exploits. Gaining power, doing ancient Sith rituals etc. so it's a very different feel, some hate it as its completely irrelevant to th 'Star Wars'-ness, but it again is fun to see a different perspective and take on things
Chapter 1 for SI is only wierd if you choose a Twilek or Chiss (if you know the story behind the Chiss anyways) for obvious reasons to those who've played the SI storyline.
Chapter 2 was a bit meh, buuuut, it had some good parts, but, imo anyways, it started out weak.
Chapter 3 was great! And love the idea of a Sith who is more out for themselves and not out for the Sith or the Empire itself.
SI just has some really great moments, but like all the storylines I've seen so far, it does have it's flaws.
It's a storyline one doesn't want to play purely DS imo. And Chapter 3's count down scene (I think it can be avoided if you choose another chat option tho) was just GREAT! And those who've played it, should know what I'm talking about
SI was less the EPIC HERO (or villian if you choose to look at it that way) and more the story of an adventurer/pirate type.