What content is that? Sure the dialog is different because you are different person, but what big things do you miss out on? Fane does offer more history and background information, but you get a lot of that with Fane as a companion too, IIRC.
I suppose D:OS2 issue was that it wasn't a very reactive game. Players had freedom to do what they wanted but game would rarely acknowledge what we did. That's a main reason I consider D:OS2 a multiplayer game with an optional singleplayer - once you don't have friends to react to what you do, the game becomes far more static and unresponsive.
That's is not a problem unique to custom characters, but if you play as one of the companions at least some characters have a reaction to you and you get some story arc.
Custom vs. origin character might not be an issue, if the game is build to acknowledge and react to our choices, even if origins provide some unique options on top of that. RPGs can work wonderfully without rigid Bioware style story arc, if the game is reactive enough (see classic Tim Cain RPGs).