Re: It's more portable than a Macbook Air.
Interestingly, rumors have insisted for the last few months that Apple will launch some kind of 12-inch MacBook with a high-resolution screen, and possibly (and this sounds interesting/questionable, if true) an ARM-based processor. Apple's invested a bunch in sensors, so who knows... but it would be interesting.
As it is currently, I see your point about direct comparisons, but I think a number of people will end up choosing between the Surface Pro 3 and some kind of MacBook just because of marketing and similar pricing. So the comparison is also unavoidable. The Surface Pro 3 scales content such that you see 6% more on its 12-inch screen than you do on a 13-inch MacBook, and whereas I frankly find the 11-inch MacBook Air too small, the 12-inch Pro 3 seems fine. So I don't think screen size is necessarily a reason to invalidate comparisons.
But the comparisons are difficult for other reasons because the devices overlap and diverge in so many ways. The Surface Pro 3 will be awesome for certain use cases, especially with the pen, and can certainly function as a laptop. But for general users who don't care about convergence and just want a kickass laptop, the 13-inch MacBook Air is an excellent machine. If you're looking at the Surface as a light, thin laptop, rather than some kind of hybrid, it's very nice. But the high-end model costs as much as a MacBook Pro, and I don't think the Surface will match any of the MPs in power. The Pro 3's computing muscle compares better with the Air's, but again, if you're focused on laptop use, rather than hybridity, you have to think about OS X vs. Windows 8.1 too. The Surface has touch, but the MacBook's Track Pad provides a pretty great tactile experience. And so on.