Agree with just about every word you've written here. Going into the movie, I think I may have had the same problem, expectations-wise. I guess I just saw a bunch of reviews that were throwing around the "Best Bond Ever" line and so I was oddly disappointing when it ended up only being a "Very Good Bond" instead.
While I'm not sure if the "influences" were intentional, you're definitely right that Skyfall has many parallels with The Dark Knight. Bardem is certainly a very Joker-like Bond villain in the sense that he is an outlandishly psychotic criminal mastermind, with convoluted plots that are always impossibly well-orchestrated. It's amazing how trains always show up exactly when and where you want them to, right?**
And as to your point about the Bond girls taking a bit of a back seat this time around, I hadn't really noticed it or thought about it while watching the movie, but in retrospect I have to agree. Actually, you could even argue that in a certain sense Judi Dench was the main Bond girl -- with a motherly relationship rather than a sexual one.
Overall the acting and the action are more than good enough to ensure that all the little hiccups get smoothed ever, making for a very fun experience and a great addition to the franchise. Get out and see it if you can.
**Having taken MARTA to work the last couple of weeks, I can confirm that this rule ALWAYS holds true.