I think - mostly it's the plot holes that are opened up and never resolved. The TARDIS' exploding wiped certain events from existence, such as the steampunk Cyberman mech in Victorian England and pretty much every mass invasion of the Daleks. I'm cool with the former, since it was a stand-alone episode, but the latter just leaves way too much unanswered. Like, when the Doctor came back into existence, did the TARDIS' explosion undo itself as well, and did all those events come back into being? And if they didn't, what does it mean for Donna (who, without Dalek interference, wouldn't become the DoctorDonna and have her memories wiped), or Adelaide Brook (whose close brush with the Daleks inspired her to go into space and, furthermore, is "a fixed point in time"). Did Mickey, Rose and Jackie come back from Pete's World, and if so did Mickey decide to stay around? Are he and Martha married? And this isn't just my love of Mickey speaking, either. I'm having trouble telling if the finale was written this way by accident, or if they intended to restore the status quo from the beginning.
There are a few other things here and there, and while the plot holes are the ones that bug me the most. I'm also annoyed at the presence of Cybermen and Daleks in the "lock the Doctor in the Pandorica" scene; we knew that some Cybermen were able to escape the Void and did an emergency temporal shift, but they never went out into space (that I can remember). If it had been some of the retro Cybermen, then I'd understand, but these were the Pete's World Cybermen; the implication had been that they were all dead/in the Void/still in Pete's World Or Something. I wouldn't have minded if there had been some sort of indication earlier in the season that they were still around...let alone how they managed to time-travel so precisely.\
(Then again, there are a few other Cyberman-related plotholes, such as the body in the Pandorica tomb being able to operate without a brain inside.)
I also vaguely remember some Daleks claiming that, as long as all other species were destroyed, it didn't matter if the Daleks died as well. I'm not sure if that was the scavenger Daleks at the end of Series 1, or the Cult of Skarro, or the ones on board the Crucible...hell, I could even be imagining it...but I remember the sentiment being there somewhere, so the Daleks collaborating with other alien species to lock the Doctor away didn't make a lot of sense to me.
All that said, however...it was still an enjoyable finale if you're willing to overlook the plot holes and mischaracterizations. Much wibbly-wobbly timey-wimey antics, and Auton Rory, and the fez. I like it the same way I like the S4 finale.
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I think - mostly it's the plot holes that are opened up and never resolved. The TARDIS' exploding wiped certain events from existence, such as the steampunk Cyberman mech in Victorian England and pretty much every mass invasion of the Daleks. I'm cool with the former, since it was a stand-alone episode, but the latter just leaves way too much unanswered. Like, when the Doctor came back into existence, did the TARDIS' explosion undo itself as well, and did all those events come back into being? And if they didn't, what does it mean for Donna (who, without Dalek interference, wouldn't become the DoctorDonna and have her memories wiped), or Adelaide Brook (whose close brush with the Daleks inspired her to go into space and, furthermore, is "a fixed point in time"). Did Mickey, Rose and Jackie come back from Pete's World, and if so did Mickey decide to stay around? Are he and Martha married? And this isn't just my love of Mickey speaking, either. I'm having trouble telling if the finale was written this way by accident, or if they intended to restore the status quo from the beginning.
There are a few other things here and there, and while the plot holes are the ones that bug me the most. I'm also annoyed at the presence of Cybermen and Daleks in the "lock the Doctor in the Pandorica" scene; we knew that some Cybermen were able to escape the Void and did an emergency temporal shift, but they never went out into space (that I can remember). If it had been some of the retro Cybermen, then I'd understand, but these were the Pete's World Cybermen; the implication had been that they were all dead/in the Void/still in Pete's World Or Something. I wouldn't have minded if there had been some sort of indication earlier in the season that they were still around...let alone how they managed to time-travel so precisely.\
(Then again, there are a few other Cyberman-related plotholes, such as the body in the Pandorica tomb being able to operate without a brain inside.)
I also vaguely remember some Daleks claiming that, as long as all other species were destroyed, it didn't matter if the Daleks died as well. I'm not sure if that was the scavenger Daleks at the end of Series 1, or the Cult of Skarro, or the ones on board the Crucible...hell, I could even be imagining it...but I remember the sentiment being there somewhere, so the Daleks collaborating with other alien species to lock the Doctor away didn't make a lot of sense to me.
All that said, however...it was still an enjoyable finale if you're willing to overlook the plot holes and mischaracterizations. Much wibbly-wobbly timey-wimey antics, and Auton Rory, and the fez. I like it the same way I like the S4 finale.