I think it's on purpose. I believe what Larian is trying to say by giving all the companions unique, out of the ordinary backstories is that they were purposefully selected by the "Absolute" and that the abductions weren't random. The biggest question is, can they make the MC's backstory just as unique? I certainly don't want no God Chosen crap from DOS2. That's what's really missing right now, is the backstory of the MC. Without a backstory, the companions "outshine" your MC and I think that's what a lot of people don't like. That's what I believe anyway.
That's a good point about how the MC and the companions seem to be Chosen Ones by the Absolute for some nefarious purpose. Among other things, it would explain why we're not transforming on the usual schedule, and why other NPCs infected with the tadpole lose it when they die. It makes for different adventuring party dynamics than a typical CRPG. The companions are a bit more colorful and not just subservient to the player main character.
Most of the complaints I've seen are either based around not having a preferred romance option, or having so few companions that we can't put together an optimized party based on preferred "alignment." That's just a trade-off for having fully animated cut scenes and voice acting, which is resource-intensive for a small game studio. We're not going to have dozens of choices here.
Personally, I'm not stuck on the idea of having an all-Good aligned party, and romance isn't important to me because it's seldom done well in this kind of game anyway. I could go through the rest of the game with my current party of Lae'zel, Shadowheart, and Gale with my MC Rogue without complaint. And we haven't even seen the remaining 4 companions yet.
