While I'm no expert on the lore, there were a few things that annoyed me about the final episode. Simeon shows up practically out of nowhere, the Whisper Men are either actually related to the Silence or just very unimaginative considering, and I'm probably missing something major here, but why wouldn't the Great Intelligence have killed the Doctor (and thus necessitated Clara's saving him) in all his incarnations, especially the Time War? Either Clara doesn't remember what she did in her copies (which sounds about right) or the Great Intelligence didn't have the time to kill him every opportunity he got before he was destroyed. As you can see, I'm not very well versed.
My other criticism is pretty common across this series. I practically have to take the show's word for it when the Doctor is in intense pain, because it's often from some sort of nebulous source. As in he's never in any physical pain I can relate to. Apparently he was dying all at once, but what does that even mean? Is he just feeling all the individual sources of pain? Why would he not just die practically immediately due to the circumstances of the quickest death? I just find it really hard to believe he was literally killed in many different ways at once and that caused him a merely monumental amount of pain instead of...killing him.
Last thing, which could just be a bit of character building, he's not very insistent about Clara not saving him. He just sort of goes "No. No, please. No". Doesn't offer any arguments. If he'd really wanted, he probably could have summoned the strength to restrain her or kill himself somehow. I choose to think that he secretly just knew it was the only way he was going to live and let her do it.
sanquin said:
-The whispering things, what were they? Never explained. They were just there for the sake of the episode working.
-The prisoner in the beginning. Who was he? How did he know what he knew? Never explained once again.
As far as I know, the Whisper Men are forms the Great Intelligence can control and serve as replacements for Simeon's body if it is destroyed (which it seems to have been already seeing as the Simeon that shows up is empty), and the prisoner could have been the Great Intelligence taking on a form other than Simeon? I've got no idea if it can do that, but it imitated Simeon well enough so I don't see any reason why not.