I think that the origin system, because the companions are now a lot more fleshed out and have interactions with each other/the approval having a much bigger say in their reactions to you, is ultimately an atavism that would only work against the game in the end.
I think (hope, at least) that they've restricted the origin characters from being selected in the EA specifically to gauge as to whether or not it should stay in the first place, because, in my opinion, having a lot of options for custom characters to shape their own stories in a unique way over a bunch of tailor-made ones that work better if you are an observer/side participant is pretty much a win on all fronts. You could still have unique dialogue options/scenes if hot-swapping characters in conversations is implemented, similar to how NWN2: Storm of Zehir allowed you to use your NPC companions here and there and they had unique interactions. You could allow the player to see their illithid dreams by taking the option to probe their minds, and so on.
Since it's now confirmed that there are non-origin companions as well (Minsc & Jaheira for the "good" route, potentially Minthara for the "evil" one), the distinction becomes even more arbitrary. Just make everyone a companion and allow the player a greater range of interactions with them over restricting interactions to playing a specific character. As much as I absolutely love D:OS2, having to play it as either Lohse or Fane to get the fullest picture of the story is a big bummer, because they work really well as companions and losing out on those interactions in exchange for a more coherent storyline is not exactly a pleasant deal.
