A few points. The stolen "agent list" isn't forgotten mid film - by then it's done its job, which is to lead MI6 and Bond in particular to Silva to allow the latter to be captured and put his assassination plan in place. Up until then it's part and parcel, right down to the BBC News broadcasting the death of an MI6 agent on the list.
Getting on that yacht - Bond tends to be good at that sort of thing, he's a trained agent, and its not the first time in the films he's gone from one place to another with no linking scene. (In TMWTGG, Bond goes from an agent in shirtsleeves who's dropped his gun, to a "dummy" in suit, collar and tie who suddenly turns round and shoots the villain. How did he get there? We aren't told.)
Severine's death is a shocker, and Bond could have done more to help. Admittedly, she's no angel, setting up a man to be assassinated by Patrice. But more could have been done for her. (A bigger plot hole is how Silva could have planned that 1. fragments of a bullet in Bond would lead him to Patrice, 2. that Bond would catch up with Patrice, 3. that in the event of Patrice being killed rather than questioned Bond would know where to go next - the Macao casino. Then again Silva's plan didn't bank on Bond being shot by his own side.)
Q plugging into Silva's laptop. All those warnings about computer bugs and viruses ignored! Silva was clearly banking on Q's curiosity getting the better of him.
The London scenes - what I found curious is how Silva would know that M was appearing before the enquiry, and all that followed depended on it.
The showdown at Skyfall - I liked the idea of the villains attacking Bond's HQ rather than the usual order of things. That said, heading up there expecting to find the gun cupboard fully stocked and not having backup probably wasn't a good idea. One plot problem which, as I recall, a Member of Parliament who had seen the film pointed out was that, having deliberately put the head of MI6 in harms way, Bond would be up on a disciplinary and be lucky not to be sacked or worse.
Finally, Bond's drink problem and going AWOL. It's not being disrespectful to Fleming's creation, it's "character development". Ian Fleming himself, in his last two novels had Bond go far from what we expected - "hitting the bottle" and being on the verge of a breakdown following Tracy's death, losing his memory, then returning to London as a brainwashed assassin. I think there were hints, in the pre title credits before he got shot, of tension between M and Bond. It looks like being (accidentally) shot did it for him, and only by watching TV in a drunken haze did Bond come to his senses. Now there's a bit of a plot hole - Bond only finds out about MI6 being blown up by chance through 24 hour rolling news?
I should add - none of the above ruined my thoroughly enjoying the film!