I think the Inquisitor has one of the best storylines in the game. Some people disagree, but I think it just comes down to what you're looking for in the storyline.
The story is about a rise to power. It's not about being some great Sith right from the start...and it's definitely not a "Palpatine story" as some people feel they were led to believe.
Just to offer another PoV, I will wholeheartedly disagree. I've played the following stories through the CH3 completion:
- Bounty Hunter (almost twice)
Of all those, by far with a massive margin, Inquisitor was the worst, IMO. It was the only story where I felt like a petty moron, instead of a hero or bada** (depending on light/dark). Time after time in the Inquisitor story I sat there dumbfounded as to why on earth the character would make those decisions, given what had happened already. Chapter 2 in it's entirety felt like a pointless foray into the absurd. The only thing I will concede is that the Inquisitor story is VERY true to the sith mantra.
And don't get me started on companions. Inquisitor had the most shallow companions in the game. The padawan you get is so much worse than the Warrior's story line. The only decent companion is the last one, and you have him for effectively one planet of story.
On the other hand, bounty hunters have a satisfying (if not a little predictable) story where you actually feel quite awesome. The companions make sense, and are often quite hilarious. Plus, the story seems equally satisfying as light or dark.
EDIT: In terms of DPS, you really shouldn't be worrying about that right now. There will be massive balancing coming soon, and which class is at the "top" changes very often. You should play the class that is the most fun to you.