Sam Mendes meant to loop Skyfall with Dr. No. He stated that in interviews and said something to that effect when discussing the final scene in Skyfall on the Blu Ray commentary.
In that final scene, we have Bond and Miss Moneypenny in Moneypenny's office from 50 years ago. We then have that padded door, opening onto what is essentially M's large office from 1962, with the desk in front of the mantle. The only real discernible difference is that both Moneypenny's and M's offices are not as brightly lit as the old days, and, of course, the painting of the destroyed (or damaged) MI6 building replacing the naval painting behind M. However, the other painting is a naval one, and is clearly seen as Bond stands there.
While Gareth Mallory is really not Miles Messervy, and apparently served in the Army and not as an Admiral in the Navy, for all intents and purposes, given the set, they are meant to represent the same person, and it appears as if we are meant to think that Bond's next assignment will be to investigate Strangway's disappearance. We are at the point where these three films serve as both a reboot of and prequel to what has come before.
Now there is plenty here which does not make sense, such as the changing races of Moneypenny and Felix, Judi Dench's M serving both after and before Messervy/Mallory M, Bond meeting Felix Leiter for the first time twice, the technological advances of the last 50 years. However, just look at Bond and Blofeld meeting for the first time in two subsequent films for continuity discrepancies before the reboot, and you will see that this ultimately is no big deal.
I think that this allows for the timeline to be interpreted in several ways, and one may place the adventures in whatever order they see fit. One may also wish to still look at these three films still as a separate series, despite Mendes' intentions.
I was one of those who was against the reboot, and while still appreciating Casino Royale, thought that Quantum of Solace was the absolute nadir of James Bond. Skyfall completely changed all of that, as it signifies that Daniel Craig is playing the same 007 as Sean Connery and George Lazenby and Roger Moore and Timothy Dalton and Pierce Brosnan. It is a true 50th anniversary celebration, merging the old Bond and the new.
At the end of the day, and I realize I was as guilty of arguing to the contrary as anyone else, continuity may really not matter. It probably means more to Sam Mendes then Barbara Broccoli and Michael Wilson. However, the fact is that Skyfall has made a billion dollars. I am sure that at least part of that was due to people glad to see that the old Bond was back.
Here is to another 50 years!