I think the OP raises some valid points, albeit from an immersion point of view. There will be always be an element of this quandary in a party based CRPGs ie. why do other party members hang around waiting but it is inherently more so a problem in BG3 when you consider the main hook of the storyline which revolves around the ticking time bomb of the tadpole inside our heads. Time is apparently of the essence yet they will still wait around indefinitely...I couldn't tell you how many days pass because there is no truly accurate calendar in BG3 (the journal counts days, but you can long rest and it doesn't affect the days in your journal). It just makes for a narrative that creates all sorts of issues in this respect.
I'm not really sold on the concept of the other companions lacking initiative; I just think it is poor storytelling. In previous BG games if a companion felt your goals didn't align with theirs they simply left, which makes far more sense.
Regarding characters dying while doing their own thing, Wyll can die the very first time you encounter him at the battle outside the gates of the Druid Grove. I always thought that it was rather daft that one of your potential companions can die before you even get the chance to meet him properly. Maybe it has changed since I last played, I don't know.
Well, the character should know that your goals are really different. So Gale leaves if you don't give him magic items, and Will leaves if you destroy the grove. Is it logical? Yes. The rest leave only if you really mess up your relationship with them, which, again, shows your priorities. By the way, if you save the grove, but do not take Will with you, then he is very offended and speaks out about it at the party.
Perhaps the first act is not enough to make your relationship deteriorate so much.
Killing the characters so quickly is the worst solution. This is what was in DOS 2 and this is what I didn't like. It's nice to change your companion sometimes. It's always been like this, in games like Dragon Age, PoE, or Tyranny. Some companions just sit and wait for you. This is a common game mechanic.
