I think my only complaint when it comes to the companions is the initial encounter with Astarion. I do not particularly like the only options of him placing a knife at my throat, then a wrestling match only to become "friends" or "companions." Personally I feel the PC should have additional options that do not end in a knife to the throat and then becoming besties.
Additionally, I find it odd that with the exception of Lae'zel and Shadowheart, you do not see any of the companions on the ship. Gale recalls seeing you on the ship, but where was he during all of this? Why can we not free Shadowheart or meet additional companions on the ship if we are all on the same ship together. This seems rather odd to me.
With the other companions, I can see why they are the way they are, and it does not bother me once you dig a bit deeper into their actual character. Gale seems to have a superiority complex, but it goes with his background as being a prodigal wizard. Probably akin to him being better than most his whole life or having other privilege's (if that's even the case).
Shadowheart comes off in such a way that it may be interpreted as her being rude/mean etc. When looking at her closer you can see its just a front and she does it so others wont get to close/pry etc.
Lae'zel comes from a different place altogether and their rules and customs are vastly different, so I do not expect my character to understand where she is coming from, much like I do not expect her to know where I am coming from either. On a side note, I find it humorous that there are several dialogues with other NPC's regarding noses, or lack their of.
Wyll is the "hero" in mind at least and tells you his intentions as it comes to the Goblins. He wants to kill them all and should be expected to act in such away to these enemies.
Larian mentioned the other characters would be their own beings and do things when the PC is not around, so its not to hard to see why some characters act a certain way or do certain things in game.
Someone mentioned the Gur and Astarion becoming upset about it. This makes total sense because of who and what Astarion is, and what this Gur or Monster Hunter represents to him.
Personally I expect the other characters to have their own personalities and make varying decisions because this is an RPG styled game. If you were playing 5e or any other table top styled game, the DM would have the NPC's make varying statements and decisions that you would not agree with, but that is part of their charm/frustration. Not everything will go smoothly.
Lastly, on my various playthroughs, I have yet to see the other members of the party get together and say something along the lines of "You are the PC and our de facto leader here on out."
We as a PC have to learn to trust the other parties and in turn they have to learn to trust us. We do not know one another, but it seems like other people expect the characters to follow you blindly.
I've only had the knife to the throat once in 4 goes. So the options are there, you just didn't get it. How many times have you had this interaction with him? If it's only one, then how can you say there are no other options, and if it's multiple, but you're using the same dialog option every time, how can you say there are no other ways for that to turn out?