Skyfall was definitely a stand-alone story that really had no narrative or thematic connection to the plot-line that ran through both Casino Royale and QoS.
But then SPECTRE came along and did a quick and dirty retcon to messily tie the hitherto separate and disparate CR/QoS and Skyfall storylines together to take full advantage of MGM finally having the rights to use Spectre and Blofeld in film.
Kor
Big deal, and so what? The original novels were tied together too, you all forget, and they had a thread connecting one to the other. There's nothing wrong with Eon and MGM doing this except that people seem to want the silly Bond of the Moore era to come back, or at least the version of the later two Brosnan films, which might be a disaster.
Personally, I think that this Bond more than fits what Fleming was trying to do, and was a lot more realistic; this is a guy who works for the covert wetworks division of MI6, and who has a nasty job as mentioned in 'The Writing's On The Wall'. I wish that people would read the novels and get familiar with that aspect.