The alignment system really only worked for the Pen and Paper, and I would like it if Larian left it out for a system more rooted in the real world. I mean everybody generally falls in the same category, where he is "good" and abides to the rules until the conditions make him break out of it. Some just do it earlier than others. People living totally outside of the social norms are really rare.

As far as the permanent party I do not know. I mean they have this camp mechanic, where most interactions happen, similar to the Normandy in Mass Effect or the campsite in Dragon Age, so it makes little sense to just remove a significant portion of the NPCs and therefore interactions.
It also narrows the possible choices for the casual players, that have not extensive knowledge of the game mechanics, so they will just stick to the basic with no experiments. So rogue, fighter, cleric, caster (most likely the mage). So the hybrids and specialists are most likely to be left out.
Now what I find more likely is that certain origin characters drop out, for whatever reason they come up with. And I would not mind that at all, since all of them are so edgy and have a story to tell that makes me roll my eyes constantly. I bet they all are the Chosen One in some way. I would very much rather have "normal" people as my companions. Mercenaries, wandering minstrels, a ranger trying to slay evil, and so forth. Stories attached to the real world and therefore drawing their personality instead of secret heirs to thrones, possessed by a demon, vampire lord or whatelse they dream up. These are not really deep characters, they are just shallow characters with a main quest attached, like any PC.
So if two of them are gone, I would not mind, as long as I get other people to join me, that I can phase in and out and try new builds on. I am also not a fan of replayability through locking content, I do more playthroughs with often the same character where the general playthrough only changes in nuances. I very much more like the game making me sink 80 hours in one playthrough, than making me spend 40 hours in two playthroughs.