Shapeshifter doesn't change everything. I haven't used it but would imagine it changes standard widgets(scrollbars, table headers, aqua buttons etc etc), not custom ones.
Shapeshifter uses application-specific skins to replace custom application interfaces. Some themes have skins for tons of applications, like iTunes, Safari, iChat, iPhoto, iCal, Mail. And most themes are developed by one person.
And you seem to think that a large company can't do the same work as one person? You don't know how long they've worked on it, or how many people are working on it... so how can you say that they can't?
It's not really a matter of "they can't do it" .. they can. It's just a matter of "will they?"
It does all come down to one thing: Aqua is a skin. They can replace it if they want.
It may be rough to replace it, some apps will look weird until the developers update ... but the same thing happened with Intel Macs and the OS 9 -> OS X transition.
There weren't many Universal Binaries when the Intel Macs came out (I had one of the first Intel Macs; an iMac). Applications ran slow. It was ugly. But it only took a month or so for developers to release UB apps.
The OS 9 to OS X transition was longer than the Intel switch, and it was more painful, but it was for the better. OS 9 apps looked ugly running in OS X, but they worked. And people eventually transitioned.
Apple isn't afraid of transition.
I don't know if they will replace Aqua or not, but denouncing that they
can is pretty idiotic, IMO.