Your point is totally correct. The plot has all sorts of threads coming off due to companions that can't be too important because you might not have them, and really it's even worse than a game like DA:O, since in that game the groups you went to (Deep Roads, elves, mages, Redcliff) had separate concerns that had to be fixed, whereas in this game Act 2's major dungeon is all about Shadowheart, the Creche is all about Lae'zel, Astarion's absence makes Cazador a totally meaningless sidequest NPC, etc, and things are more tied to companions in general. I think they ended up with a rather unhappy medium - the companions are important enough that they can't really be dropped without hurting the narratives in all these places, but Larian insists on them being optional, also because of their multiplayer commitments as much as freedom. I'm not sure how they will resolve this in future; for me, I'd just as soon they drop the extreme freedom and co-op and make more focused narratives, but those are also the things making them unique for better or worse.
