Only plot hole from RTD's era I can think of offhand is how exactly 8 became 9. The asspull solutions to the finales is another matter entirely. Yeah, the start of "Day of the Moon" was jarring at first because it just ignored resolving the end of "Impossible Astronaut" but I didn't care after a bit when I got caught up in the plot again. They ran off, they set the plan in motion, etc. As presented if they'd shown the transition the tension for the second episode start would have been lost. Why they didn't flashback to it afterwards, who know?
I'm actually talking about the basis of whole arc plotline (Impossible Astronaut/Day of the Moon/Good Man Goes to War/Let's Kill Hitler/Wedding of RS)
Watched as a whole, there is much to enjoy - Moffat is great with dialogue, characterisation, imagery etc.
Unfortunateley everything that goes on revolves around one basic plotline - the Silence/Kovarian/The Church want the Doctor dead, and they have a plan to achieve this.
A plan that makes absoluteley no sense.
They intend to abduct Amy's daughter, who is part Timelord, and programme her to asassinate The Doctor. Why?
Melody is one woman with no superpowers other than being strong, smart & able to regenerate. The Silence have endless numbers and are impervious to memory, with built in energy weapons. All they have to do is wait until the Doctor's back is turned, and adios muchasos....
...Anyway. I guess she has her reasons. Kovarian successfully outwits The Doctor at Demon's Run, and makes off with Melody in her spaceship. Does she head off to a secret destination to train Mel and arm her with some awesome 25th Century superweapon?
No. She timetravels (???) back to Earth in 1969, puts Melody in an orphanage, and waits for the Silence to manipulate mankind into making a spacesuit that they can then update with alien technology that can remote-control Melody into killing the Doctor with...an awesome 25th Century superweapon.
Say what?? :confused
Okay, okay, presumably Kovarian has been training young Mel at the orphanage, with homicidal tendencies...in case the remote control spacesuit weapon doesn't work?
Well, no, actually. When Mel faces up to The Doc in her robosuit, all she does is cry for help, then eventually escapes from the suit and runs away.
Hiding out for six months, she eventually gets sick, and regenerates.
At this point, things get a bit vague. Either she regenerates into young Mels, somehow suspends ageing, then hangs around for 30 years or so, gets in to school with young Amy and resumes ageing OR she regenerates into another form, hangs around for 30 years, dies again, and manages to regenerate into young Mels, somehow controlling the exact age of the body she regenerates into, so as to be the same age as Amy.
Anyhoo, whatever, she does one of the above. Somehow, somewhere along the line, she's realised she has to kill the Doctor, despite having the opportunity to do so back in '69, and decides the best way to do this is to hang out with her mum for 15 years, so as to get an introduction to the Doc. I don't think she's actually as good a buddy of Amy's as she thinks tho, as she misses loads of opportunities to meet the Doctor, and Amy never mentions her bestest buddy to her time-travelling chum.
Still, all works out in the end, and she gets on the Tardis. Pity she didn't practice shooting during her 40 years of hanging about, as she manages to shoot up the Tardis instead of the Doctor.
But wait! Mels gets wasted by Nazis, and regenerates into River! We're on the home stretch!! She's still homicidally intent on the Doctor (I think she's just pissed at having to sit through the 70's) and she does a pretty good job. Unfortunateley she falls in love with him at the last minute, and thows away the rest of her regenerations to save him from the poison she just gave him!
Damn, Kovarian, how could you have predicted that your tightly laid and infallible plan could go so wrong?!?
So River and her mum forget about each other, and get on with their lives.
Unfortunateley for River, Kovarian is determined to get her back into that damn suit.
So much so, that instead of getting one of her crack marines to get in there and waste the Doctor to death at his fixed point in time, our newly graduated professor is once more hijacked for the job. For some reason. Your guess is as good as mine...
Of course, rotten ole patch-eye reckons without the power of love! As we all know, fixed points in time mean nothing to time lords when it suits them, and River manages to split time into two streams (err..I think) so that all time is happening at the same time at another fixed point, and this is far from good. The Doctor has to die!
Except he doesn't have to. By putting on a robot Doctor suit, marrying River, (despite the fact that he doesn't want to, and she's embarassing him) and then kissing her, he can restart time and live to fight another day, under an assumed name (The Dentist?)
Hold on a sec...if he's actually in a Doctor suit, then it's not actually him kissing River, it's the robot. So time shouldn't actually restart at all...
Oh well, I guess we can forgive one little bit of illogical plotting :angel