Alrighty, first off, good to be here. Really looking forward to TSL.
A while back, I hosted a game online using Vampire the Masquerade: Redemption, and built a very long game where each player in my game had a unique talent. I've heard this idea is already addressed in TSL, so I don't need to get into it, but it gave me a lot of practice in honing those Dark Side type characters.
The first thing, and I believe this fits into Star Wars as well as most good stories, is having the villian with a more complex motivation than just 'I want to take over the world/galaxy/universe/multiverse/ just because it's there and I need that space for my ego.' Nobody in Star Wars just woke up one day and became the Dark Lord of the Sith, unless they were a psychopath to begin with, anyway. They all took little steps to get there.
All I'm saying is, I'd like to have an actual, personal, history behind the main badguy, why he or she has gone to those depths to become such a monster, if they are.
Here's some do's and don'ts I learned to follow when making a deep, complex, interesting and dangerous badguy.
Don'ts.
1) Don't overuse them in appearences. They should only appear when needed to advance the plot and even then they shouldn't actually fight the PC or the party until it's time for the final battle. We can watch him in action, like seeing the new Sith Lord blow away an entire regiment of Republic troops with Force Storm, but to overuse the badguy weakens their impact.
2) Don't allow something to diminish their impact when they are introduced or used. While one could have the option to taunt the badguy to throw him/her off balance before the fight, if that option is going to be there, ensure he/she has a decent recovery, or it'll just be foolish.
3) Don't have the Sith Lord leave a single notepad lying around explaining the entire plot away. That's rather annoying. He might as well have a five year old child advisor, too.
Do's.
1) Make them intelligent. I've nothing against a stupid enemy, but stupid enemies aren't going to climb to the top of the Sith ladder. If the person is brutal, then make them so, but at least make them able to be dangerously smart on when to unleash that brutality. Bonus points if the badguy can get the goodguys to do the dirty work with only a few hints as to what's going on. Misdirection is important, especially in times of war.
2) Have them change their tactics depending on what the PC is doing. If your PC is climbing the ranks of the Sith, have a different encounter in a different place at a different tone, than you'd have if your PC is fighting for the Jedi. Bioware messed up here, I'd hate to see a repeat of that. I'd suggest for a Darkside ending, the fight would be on Korriban where you try to wrest control of the Sith from the other Lord, after you've gone through the others of course. But for a Lightsider, the entire scenario could be different, say, you infiltrate the base and are forced to face him/her without support or backup.
Anyway, those are my two cents. I'll add more later, please review!