The companion system in this game was one of the things that set this game apart, gutting it is a huge blow and there's really no replacing it with simple op battle bots (elementals) or temporary npcs that only hangout for a quest.
Yeah, but the main problem is that the way they were implemented increases the complexity of character interactions exponentially. It's not really due to any coding issues, but rather due to the innate complexity of the game world and mechanics, and all of that time and effort would be going to content that the majority of players are unlikely to see.
For example, the interaction between Brax and Sean in Slaver Alley has dialogue for Brax, Bree (femme Brax), and Brandi (subby, bimbo Brax), with lines for Brax with a covered mouth, as well as Brax-specific pregnancy reactions. This is on top of the various reactions to the player character, which all have their own unique dialogue, and the more you build out the world the worse it gets. Even AAA RPG like Mass Effect, with massive teams and EA-sized budgets, aren't that bold when it comes to character interactions.
That said, I think removing the feature altogether is a bit much. I think a more balanced approach would have been to allow for companions but largely leave them out of the NPC dialogue altogether. It would make things a bit less "personal" but it would remove a great deal of complexity while still letting the player wander around with someone that has a bit of personality.
Hey hey, mod idea! Maybe make it so that as the player move around they occasionally make comments about the area that you're in. For example, walking by the Enforcer HQ with Brax might give a certain reaction depending on his affection with you. If he hates you, is disobedient, and is still dommy, he'll make his bitterness well-known. If he likes you, he might remark that, slave or not, getting to adventure with you is better than the daily grind ever was. It would make it feel like you were building a relationship with the NPC rather than them simply being a set of stats on a computer screen, yet it wouldn't be nearly as bonkers as trying to create complex NPC<->NPC relationships.