The problem goes away if Larian have another 10+ characters up their sleave. Given that it's most likely 3, I agree it's a problem, but given that the same people who wrote the characters would be tasked with changing/modifying them, it's probably a lost cause. And again, it's not because they're evil - I play/have played evil or neutral characters with evil/neutral companions more often than not - they're just a bit lame. Making them slightly nicer doesn't really change that.

Gale and Astarion seem designed to be dislikable, which they are. Mechanically Gale is a disaster - "let me destroy your good items because I'm a moron. Also, I'm really smart and you're not"
Lae'zel is a wasted opportunity in getting you to sympathise (through shared ship-experience, forced to help each other, mutual respect from that) with someone who is evil. As is, she forgets the ship thing, barking orders rather than trying to convince you as a "friend"/"one of the good ones" to use other people/companions, show strength, murder people etc. After all, you don't know them, you're almost as much of an alien in this part of the world as she is.
Shadowheart is Shadowheart. Pouty, melodramatic, like an unwanted teenage daughter. The lurking manic-pixie-dreamgirl arc only adds to it.
Wyll is nice but so naive that the cliche warlock story is dry so far.

To be fair, the small changes did make Shadowheart seem less needlessly confrontational, so props for that.

An easy change would be to get rid of most of the X approves/disapproves. It's one thing to have companions that react to your actions, and another to feel like you're constantly under inspection at work.