The theme of Skyfall is the conflict between the old and the new. You can tell because every third line of dialogue reminds you of this.
I think the trouble is that the writers and director don't seem quite clear on what that premise actually means.
Does Silver represent the new, because he is a computer hacker and a new kind of enemy? Or does he represent the old, because he's a Cold War-era agent who's gone rogue for reasons that are entirely tied to the way M has run MI6?
There's also the question of the contrast between the original Bond films and the Craig-era ones. This movie makes a big point of bringing back the trappings of the original films -- Moneypenny, Q, a 1960 Aston Marton with machine guns -- but it also makes a big point of how the original movies felt a lot more high-tech and futuristic than the current ones. (The gadgets Q gives Bond are "A radio and a gun -- not exactly Christmas, is it?") So which is the old and which is the new? And that's before you even get into the point that Craig's Bond, and Casino Royale as a whole, are throwbacks to Fleming's novels, the oldest version of Bond there is.
There's another conflict between the old and the not-quite-so-old: the last two Bond films seemed intent on introducing Quantum as the new, non-infringing version of SPECTRE, a shadowy organization that would pose a recurring threat through the rebooted franchise. And then, in Skyfall? No trace of Quantum at all. We're back to isolated, one-off villains -- perhaps because someone at the recovering-from-bankruptcy MGM realized that self-contained movies without recurring villains just make more sense for the film franchise. (Hell, even when the old films were using Blofeld as their go-to villain, they still had a different actor in the role every time; it may as well have been a different character.)
On the whole, though, it all hung together pretty well; I thoroughly enjoyed the first and third act. (The second act was stupid and had Magic Computers. I don't know where the writer picked up the phrase "security through obscurity", but apparently he missed the part where it is not an expression any security professional would ever use without sneering. The less said about the movie's idea of data encryption and depiction of code as a stupid-looking early-1990's wireframe screensaver the better.) But nonetheless, perfectly decent. Though I'm kinda glad I waited to see it at the cheap theater.