My personal thought (and this is ONLY my opinion) is that we will No Longer Have Chapter Traits. I feel that instead, we'll end up with special Detachments specific for each chapter. For instance, an Ultramarine Detachment will probably look VERY similar to standard Force Org/CAD, but offer the tactical options that is currently a trait, as a new Command Benefit. Imperial Fists might offer more Elites, and require a set of Sternguard. Command Benefit would be Bolter Drill. White Scars may not require troops, but instead demand some Fast Attacks, and give Improved Jinks, or some such.
I'm sort of expecting a very similar thing for Craftworlds, also.
There is a lot of potential for some very cool concepts there. For example, Codex Astartes complaint chapters might have more traditional chapter set ups, while non-complaint chapters will be a bit more stylized.