I think that in discussing Larian's origin character system, it would be illustrative to compare them to the companions in Dragon Age 2. They are among the most independant companions I've come across in an rpg in the sense that their stories do not, as a whole, revolve around Hawke or what Hawke is doing. They all have their own lives in Kirkwall, and they're getting on with those lives while occasionally bringing you into them. In theory, most of them would continue doing what they're doing without Hawke's existence. Merril would still get banished from her clan, Fenris would arrive in Kirkwall after fleeing his master, Isabella would still steal the Qunari tome, Varric would still be doing his business stuff, etc. But Hawke's involvement in their stories is absolutely pivotal. Their stories fundamentally change thanks to Hawke's presence. From Varric being able to fund the deep roads expedition to Isabella potentially changing her ways and returning the tome she stole. Even if you assume Aveline could get to Ferelden on her own, it's only thanks to Hawke that she becomes a guard captain or meets the man that becomes her husband. And then there's the main story itself. Arguably, there isn't truly a driving goal to DA2. It's about the life of a refugee trying to make their way in their new home, and along the way they get caught up in things that are bigger than them. Part of the point of the story is that Hawke really is just a nobody. Just a person in the right place at the right time. Yet the story is unquestionably about Hawke, with her companions being her supporting cast, emphasis on supporting. Therefore it can be personal and strike at Hawke in ways that are specific.
Compare all that to Origin characters. By their nature, their quests need to work in such a way that they can happen without the outside influence of a main character, because they could potentially be the main character. And the main story has to be one which is at its core, impersonal, external. Because otherwise it can't work. And that's the problem I think there is with Origin characters as Larian conceives them. The only way for them to work is by diluting the story and making it something removed from the character, unable to be as personal as a story where there's one character that the story will revolve around.
This right here.
The problems with the Origin system are very subtle but systemic on a deep level. Most people don't realize what it does to the narrative at first. I didn't when I played DOS2 as my first serious cRPG, until I explored the genre and realized how the system just made the DOS2 companions and the overall narrative extremely dull in comparison.
DOS2 companions, when they interject in conversations at all, only do it during their personal arcs, or only have very generic quips about what they would decide to do in a particular situation. There's insane amounts of missed potential here. Probably the most interesting interaction they have between each other (or the ONLY inter-party interaction I can even remember, for that matter) is when Sebille and the Red Prince have a brief scuffle about Sebille assassinating the dreaming lizard towards the beginning of the game. But it's telling that even there, they don't confront each other about it at all on their own, they just complain to you to hear what you think, and then this never gets brought up again thereafter.
One would think that Ifan would have things to say to Sebille about her being the Prime Scion and the potential future of her people, given that Ifan was indirectly responsible for nearly genociding the Elves. Or that Beast would have advice on how to govern for the Red Prince, for when he and the Princess assume the throne of the Lizard empire in the future, lest he end up with rebels like Beast making life hard for him.
I guess what I'm saying here is that not only does the origin system come at the huge detriment of custom characters, Larian's specific handling of it ALSO comes at the detriment of the actual development of the companions and the party banter that can reinforce said development. Not only are the origins clashing with custom characters in importance, they also clash with
each other in the end.
Alexander could have been a secret companion that could have joined the party at the end of Act 3, instead of being immediately killed off with the obvious betrayal by the other antagonists. He had the potential to be a very popular and memorable character and would have been THE big spoiler/plot twist of the game, because if there's one thing that mass media likes, it's former enemies turning into allies. He could have also come with such a hilariously overpowered kit that he could have attained the same level of notoriety as Thunder God Cid from Final Fantasy Tactics. But the Origin system combined with the decision to kill off all inactive party members at the end of act 1 made this impossible. Imagine what Alexander joining the party and going through actual character development, along with the lack of the awful design decision at the end of Act 1, would have done to improve the highly lambasted narrative of Act 4. Imagine him confronting Lucian at the very end of the game and realizing just how badly he had been played by even his very own father the entire time. When you really think about it, it's clear that everyone trashing how Act 4 was constructed is actually a direct consequence of the Origin system and the end of act 1 culling, because Larian at that point had massively written themselves into a corner.
People fear that BG3's narrative will fall apart later on with this historical context, purely due to entirely avoidable gameplay design decisions baked into the game's core.