#1 Who were these people? Awesome episode, but where the bloody hell did eyepatch lady and her giant, giant army of religious warriors come from? We've never seen her or them before and I have no idea WHY the hate the Doctor enough to form an entire army against him.
Well, we've seen the army before, in the Angels two-parter. I imagine more will come later. They mentioned a war or two going on (the Headless Monks were "Heaven-Neutral," IIRC, and Eye-Patch told the Doctor there was a war against him). If this were Babylon 5 or something where they were better about keeping track of their loose ends, I'd imagine there was some kind of 51st century metastory going on that would ultimately tie in the Anglican Marines, the Time Agency, the Library, and the other stuff we've seen (I'm pretty sure its the only time period the new series has dealt with on an ongoing basis aside from present-day).
#4 Why didn't the Doctor go calling on Captain Jack for his team of allies? Seems like the perfect man to fight this battle.![]()
Ooh, ooh! 51st Century metastory! Young Jack's already part of events as Time Agent!

#5 If the Big Blue Guy (not gonna try and fail to spell his name) dies here, then how does he give River her vortex manipulator in the Pandorica Opens? I thought River was travelling backwards, meaning that each time we see her she knows less. She should not yet have her vortex manipulator, and thus Big Blue Guy needs to still be alive.
Like you said, the Doctor's a time traveler. Just because Blue and River are contemporaries doesn't mean that the Doctor had to pick them up out of the exact same moment. Also, River and the Doctor aren't necessarily meeting directly backwards every time. We shouldn't assume every time we see her is earlier in her life than the last. After all, she had a vortex manipulator in this episode and in the Astronaut two-parter. It's not necessarily the same one, but then again, it's not necessarily not.
Either way, Blue was definitely a Blue from after when we saw him in the Pandorica episodes, and River might've been. Or she might've been an earlier version, and she just steals another vortex manipulator every time she needs to nip out of prison to pick up some fresh bagels and milk.
#7 "This is the day he finds out who I am." She says this here and in the past as though it is a BAD thing, but it was rather good, wasn't it? Cheered the Doctor right up from his momentary mental depression or whatever.
We shall see. "Let's Kill Hitler!" sounds like a rather un-Doctorish thing to do, you know...