Originally Posted by
Fencers
The only question you need to ask yourself is: "Do I want to tank at some point?"
If yes, then the only choice is Juggernaut. Otherwise, Marauder.
Well, Jugg & Mara also have very different DPS styles (minus Rage, but meh, Rage) so it's a little more complex than that. Annihilation, Carnage, and Vengeance all play very differently and some people do prefer Veng.
I'd say the decision tree is more like this:
Do I want to be a melee class?
Do I want to play Sith Warrior?
Do I want to use a single lightsaber, like in the movies?
Juggernaut.
Do I want to be able to tank / have the option to spec myself into an annoying, indestructible wall of durasteel in PvP?
Juggernaut.
Do I want strong passive durability while DPS spec?
Juggernaut.
Do I want strong clutch/burst defenses?
Marauder.
Do I want to do the
best Melee DPS possible, because I'm not satisfied with 'good' DPS?
Marauder.
Do I want to apply Mortal Strike / healing reduction debuff in PvP?
Marauder.
Do I have a deep need to dual-wield lightsabers?
Marauder.
Am I not concerned about any of those things?
Flip a coin.
As for the DPS specs themselves, these are the differences:
Both classes can spec Rage. Rage isn't really the best idea in PvE since it's a little underpowered and lacks a strong toolset, and is mostly about building up stacks of a buff that make your next AoE attack do enormous damage. Excellent for leveling and chewing through trash / annoying clumps of people in PvP.
Juggernaut
has Vengeance as its other DPS option. Vengeance is about using several strong attacks on cooldown as well as procs that reset the cooldown on Ravage. If you love casting Ravage, Vengeance Jugg is the spec for you. Its pace is steady, you always have something to press but you're not under a lot of pressure to keep up, either.
Jugg DPS is also simple, with nothing to manage except your spec's procs and your Rage income/expenditure.
Marauder
has two other DPS options: Annihilation and Carnage. Marauder also has to manage Frenzy, a stacking buff that's consumed at 30 stacks (by Berserk) to grant a special effect that varies by spec, making it more complicated (and perhaps more engaging) than Jugg DPS.
Mara's Annihilation spec is about DoTs/bleeds, which do armor-ignoring damage, and has procs that let it reset Rupture and apply it more often. Anni also has a special attack that does more damage each time it's used, requiring you to use it on-cooldown to avoid losing stacks of its buff and thus, losing a lot of damage output. Anni has a relatively slow, methodical style.
Mara's Carnage plays very much like a Fury Warrior in WoW (if you have used one). It revolves mostly around applying a debuff that makes your attacks ignore the victim's armor, and dumping as many attacks as you can during that period to maximize your damage. Carnage has a very fast-paced, spammy style and is good if you drink a lot of Mountain Dew while playing.