1. The Name Of The Doctor
In the final episode of series 7, the Doctor and Clara must rescue his friends Madame Vastra, Jenny Flint and Commander Strax from the planet Trenzalore, the site of his eventual grave. A post-Silence In The Library River Song makes an appearance as a ghost-like being, visible only when others are in a dream-like realm, the Doctor, or someone she has bonded to (Clara). The Great Intelligence and his minions the Whisper Men have taken them hostage on Trenzalore to lure the Doctor there so that he can open his tomb by revealing his greatest secret his name. Once there, the Great Intelligence infects the Doctor's time stream all that remains of Time Lords after they pass to destroy the Doctor at every point in his time line simultaneously.
When He Should Have Regenerated: Actually, the Doctor shouldn't have regenerated, he should have simply died. Traveling into his own time stream is something he knows should kill both Clara and himself, but it doesn't, for no apparent reason. The Doctor alludes to the dangers of crossing his own time stream in several adventures, and when Rose alters her family's time stream back in series one to save her father, we see Reapers trying to sanitize the time wound by devouring those within it. Since viewers have an entire episode as visual reference to the dangers of paradoxes and crossed timelines, it is expected that the process will cause damage. In this case, the damage should happen to the one doing to crossing the Eleventh Doctor. Theoretically, the Doctor could have regenerated or simply died, at any point that the Great Intelligence was in his timeline. With "all of his victories" being turned to defeats by the Great Intelligence, his death and regeneration could (and in many cases, should) have been happening at many of those points in time. It would have been nice to see this visualized by the appearance of regeneration energy on the suffering present-day Doctor before Clara jumped into his time stream. With a five-second explanation from Madame Vastra or River's "ghost," this would have been a more believable and emotional motivation for Clara to take the risky plunge for this man she still barely knows. So that's what I think. What do you think? Feel free to comment!