Fight Scene Failure: Part six has an absolutely laughable sequence. Jamie swings obviously wide of the mark blows vaguely at the bad guy's face, over and over and over, while a guard in the background of a fight sequence tries to escape, with a crummy slow-motion Girly Run, before one of the heroes pulls him off a slope and onto a bed onto which he harmlessly bounces.
At the time, the concept of Regeneration really wasn't as fleshed out as it is now. At the time, the Time Lords were just making the Doctor 'change his appearance' in preparation for his exile. Now, it's more or less the Time Lords summarily executing the Doctor (in the sense of forcing him to regenerate) before they exile him.
Likewise, Jamie and Zoe's fates (being mindwiped and sent back to their own time with no memory of their adventures or one another) seemed to have left a lasting scar on The Doctor, causing him to be a lot more distant to his Companions for a long time to come. But come 40-something years later and "Journey's End" where he has to be the one carrying out that fate to a Companion, despite her begging him not to? Ouch!
He tried it again later in "Hell Bent". The result is just as heartbreaking.
Narm: The slo-mo stutter in the cliffhanger to part nine:
What Do You Mean, It's Not Political?: The Time Lords ask the Doctor to choose his own face from a bunch of drawings projected on a screen. One (the one dismissed by the Doctor as 'too old') appears to be Karl Marx. Draw your own conclusions.