In the context of the Shadowrun game, the Matrix actually looks different everytime. When in virtual reality, the entire matrix works on metaphors, and those metaphors are determined by either the node you are in or the reality filter you are using. So a Renraku node might look like feudal Japan, with IC represented as samurai and files represented by scrolls; while a NeoNet node might have an abstract metaphor where files are represented in geometric shapes and IC are bizarre entities. One node might portray cybercombat as magical spells being exchanged between "mages", while another might portray it as WWII dogfighting. Furthermore, metaphors are personal, and two people might not be seeing the same thing for the same exact event.
So, if Hacker A has a reality filter with a WWII theme, while Hacker B has a reality filter for a martial arts tournament... they can face each other in cybercombat, each see their own metaphor, and still be able to match wits against one another just fine. In-game, this is all largely glossed over, and only playgroups that actually care about the matrix really explore this facet. Otherwise, it's mainly a roleplaying aesthetic.
In augmented reality, the matrix is more like a digital overlay in the hacker's senses. It likely has some translucency so that he can see past it, and probably looks more akin to an advanced command prompt or graphic user interface than it does the classic virtual matrix. I think it should be easy to pull off should they put AR in the game first. Hell, the Unity engine might even allow hacker players to open a new window in which to place all their hacking interfaces, allowing them to swap between the real and digital rapidly.
That said, I hope that the Unity engine is moddable from the client side, because that may open up the possibility that players can design their own matrix metaphors for the game.