To differentiate between the Air and the Pro, the Pro will have more USB 3 ports, the existing HDMI port, and a faster processor. The 12" MacBook will receive a price drop to encourage consumers to buy it as the entry-level Mac, with the Air being better, and the Pro as top-tier.
This makes no sense at all. Why would the Retina MacBook have a superior USB standard to the Pro? Because it's a smaller or simpler format? USB-C is practically a given on the next Pro for the simple reason that it fulfils every need. Eventually, people will look back to Type-B and laugh.
The only reason the rMB exists is to satisfy a niche market of consumers who care about form over function. This isn't an opinion, it's a fact, and the premium pricing suggests as much. That in itself is a classic mode of establishing value where there is no substance; just take the Apple Watch as an example.
Hence, with the rMB you for some reason get to choose from four colours (two of which are tacky gold options), and spend an unreasonable amount of money on something that offers less productivity and functionality that it's older sibling, the MacBook Air.
I just don't see the logic at all in that strategy, yet it's become a defining image of the Tim Cook era. It's all about image.
The MacBook
Air got its name because it served a purpose - it was the lightest Apple notebook at the time of introduction, and that was its defining feature. That's what separated
it from the regular MacBook, which was heavier and thicker, but offered better performance and I/O.
But this is no longer relevant, and it makes no sense keeping both the Air and the rMB when there is such a clear discrepancy in the features and pricing. This is why the 13" Pro remains their best-seller; it's simply the best bang-for-buck, and isn't blurred.
The only way Apple can sort this mess out is to drop the Air and promote the rMB as the new consumer model. Possibly give it a 13" screen, a second USB-C port, (Drop the headphone jack), lower the price and you essentially have the next generation Air, but without the moniker. The CPU performance isn't as bad as people might have you think, it's just needs time to catch up; like the first gen Air.
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The terraced battery worked because everything else was redesigned. You're wrong about the larger footprint in terms of useable space. Remember what was taken out to get the terraced design working. Fans. The deeper keyboard. The large logic board. Ports. Do those same things to a MBA and what do you get? A MB. The MB works not because of specific changes, but because of all the design changes working together. So no, your two things of smaller logic board and terraced batteries would not have gotten the same results. By all accounts on the rumors posted to MCR before the concept of an MB, Apple tried to upgrade the Air, but couldn't find a workable solution.
As for the iPad Pro, it's not just branding. The design, better processor, better sound and the Apple Pencil do make it a Pro tablet. as for numbers, I point you to the articles about animators adopting it and Apple's numbers from Tuesday. All on MCR too
Your highlighting the technologies that are present in the MBA, but these are overdue a redesign. There is no market for the performance that the MBA offers anymore. Those who just want to plow through everyday tasks - emailing, writing, web browsing - will find the rMB's CPU more than sufficient. For everything else more intensive, you have the 13" MBP, which is Apple's best selling notebook. Furthermore, the MBA is no longer Apple's ultra-portable.
Therefore, a 'new' MBA would essentially be a 13" rMB. But since it's unlikely that Apple will move from a 12" screen to a 13" after all their marketing about its extreme portability, and the tooling invested, the more likely option is for the MBA to be retired and the rMB to take its place.
Also, I do recall seeing the video of the Pixar team using iPad Pros. Nice endorsement, and I'm sure they enjoy using them, but it's no coincidence that Pixar have an affiliation with Apple...