I agree with folk who think this must be plot, and probably end game, related. I just can’t see why something that wasn’t intended as a plot twist or surprise story reveal would need to be kept secret for years, and why players would only find out about it after the release, if that part of the quote mentioned by the OP is an accurate representation of what Swen said.
I don't think it has to be plot-related.
There is still a lot that we don't know about in terms of game features/mechanics. This includes both specific rules-related features (Subclasses and Races that will be in the game, spells that will or will not be in the game, Ready and Dodge actions, etc) and more general video-gamey features (max level, number of companions, Day/Night cycles or not, how difficulty modes will be handled, etc). Yet Larian has had the game more or less feature-complete since Patch 7 (if I remember correctly), with each feature being in progress toward "done".
In short, Larian has been extremely stingy with information related to game features/mechanics. It seems as if they like the idea of surprising players with the game features that will be in the game (I think that if you want prospective players to (pre-)purchase your game, you should be transparent about what will or won't be in it, in terms of specs/features/etc, but that doesn't seem to be their stance).
As a result, I wouldn't be too surprised if Swen's "big secret" turns out to be a feature/mechanics, rather than a plot point.
As for the exact things Swen said, that the original poster referred to, I think it comes from
this interview.
