I've played a Sith Juggernaut to 60, a Sniper to 40, a Mercenary to 53, and an Assassin to 35. Many people say that IA has the best storyline. They are correct. However, they SUCK at combat. Operatives aren't really able to do any damage without an AMAZING tank, and Snipes, well, Snipes do LOTS of damage but have almost no defense.
I could go on for each class, but I'll just rank 'em.
Best Storyline
1. Agent
2. Warrior
3. Hunter
4. Inquisitor
Best Overall
1. Warrior. Good Story, plus a healer at third planet.
2. Hunter. Heavy Armor and Heals/Tankiness
3. Inquisitor. No defense early on.
4. Agent. Sniper: No defense, and you draw a TON of aggro. Op: You do almost little to no damage because 75% of your abilities are either melee attacks or other stuff.
Hope this helped.