One of the requirements of the time lord trait is to take on two bad traits. I've always taken that as part of the deal for the whole time lord package i.e. you don't gain any charater points from taking these bad traits as you would under normal circumstances.
How do you play it - do you give character points for a time lord's bad traits?
Depends on the Bad Trait taken with our Time Lords. If it is something pretty common among Time Lords or relatively easy to handle in character - like taking on an Adversary like the Daleks or Cybermen, or a trait like Argumentative, By the Book, or a Minor Code of Conduct; I don't give points.
But if it is something that could seriously limit the Time Lord, such as a Major Dependency, Major Slow Reflexes, Major Weakness, or Technically Inept, I'd give points.
I must admit I'd adopted the 'bad traits don't get points because being a Time Lord is pretty frickin' awesome' rule BUT...Having seen the example Time Lords in the new Time Traveller Companion Sourcebook they all seem like they have MASSES of attributes, skills and traits so I am beginning to wonder if you are supposed to give credit for the mandatory bad traits...otherwise how did these guys get to be as/more powerful than The Doctor???
A Time Lord does not automatically gain two bad traits as part of the Time Lord trait. It is required he (or she) purchase them, though. As such, Time Lords gain Vortex and Feel the Turn of the Universe as part of their trait, and do not pay for them. That's the way I've always interpreted it.
If you're concerned about unbalanced power levels, I suggest having a good relationship between the player of the Time Lord and the Game Master. A good understanding between the two and a bit of trust when it comes to story telling can help. The point of DWAITAS is to build a story together, as a team, not as individuals, so it is up to the Time Lord to know when to take a step back and allow the companions to shine.