I don't think there should be any advantage to being human. Just keep the player normal until they obtain the Fob Watch (I would prefer if you obtained this item on Gallifrey). Suggestions for Timelord advantages:

• Timelords are able to regenerate (A given really). 
• Strength, Resistance and Regeneration upon regeneration (Though they would also be given Debuffs e.g confusion, slowness and blindness).
• Timelords can breath underwater and in airless environments for longer (say around 10 seconds longer).
• Timelords have permanent double health.
• Timelords can sometimes see strange particles around recently materialised TARDISes.
• Can prime new TARDISes (Basically, in order for a TARDIS to work, it needs to be flown by a Timelord).

While there are many advantages to being a Timelord, there should be a few debuffs for them. 

What about a disadvantage of being a Time Lord would be Dalek Temporal Squads (similar to The Chase).

if you encounter this group, they will chase you through time - I'll explain more later if you're interested.

Quoted From: wodaman01 >> 

i may make a whole thread on species you can choose to be. Time Lords will still require Fob Watches to access though.

Would you mind if I used some of your ideas in my thread?