I can think of one that stands out for me, the touchpad (in both OSX & Win).
Haven't found another make of laptop with one that comes remotely close to that of my Air. May sound trivial, but its the primary input mechanism for a laptop/ultrabook when on the move or untethered.
Oh - nailed it there! I work with thousands of pdf's. The touchpad, and the ability to flip the direction of my pdf's, and edit the title of the file whilst viewing it in Preview - that alone is worth the admission fee for me... It sounds ridiculous. In reading that again, I actually hesitate in wanting to post it, but it's true. Obviously I could add to this, but wow - nothing comes close in terms of input user-friendliness...
That all being said - whereas I have yet to upgrade my MBP, and I will surely feel justified in my choosing it over the MBA when I do - the one thing that has me occasionally wishing I went for the MBA, is the width/height of the MBP front-side, compared to the tapered edge of the MBA.
I do plenty of typing on my MBP, and whereas it is not unbearable, I often find it getting uncomfortable where my palms end up resting on the front edge of the laptop, when in the typing position. Seen it mentioned elsewhere before, and never really though much of it at the time, but can now appreciate how the MBA must be much more comfortable to type on, with the way it tapers down to almost nothing at the front... Might be something to consider...