I also really, really dislike this decision. Unless there's some incredible payoff for killing off all but 3 of the companions (and no, turning them all into mindflayers isn't an incredible payoff) I don't think it's worth it. I'm really interested in seeing how, for example, Lae'zel's story evolves over the game. But if you make me pick 3 am I going to pick the most abrasive companion in the game? No, I'm definitely not.
I am by no means saying you should be able to drag along every single recruitable character regardless of circumstances. But the limitation should come from story reasons. And by that I mean organic, believable, realistic story reasons that make sense and that FEEL like they make sense. Not "rocks fall, everyone dies" story reasons that are handwaved with whatever excuse. Good reasons would include: antagonizing a companion, a companions strongly disagreeing with your actions, incompatible companions. That's already a lot of limitations. Arbitrary locking your party is just... frustrating and imo brings no benefit.
Well said. If I have to choose between Shadowheart and Lae'zel in a standoff? Sure. If Wyll bails because I'm too blatantly evil? Sure. These make for great story moments. I don't expect to be able to keep every single companion over the entire game. But trying to force "replayability" by arbitrarily locking off all but 3 of the companions really sucks.