I think a companion system would work if the companions were almost completely independent of their actions. I'm not a huge fan of micro management of squads and all their levels, progression, stats and gear. Its not really about being lazy or wanting a less than stellar RPG system for companions, its needs to be more natural. I just find it more enjoyable when your companions have their specialized uses for various situations. I wouldn't mind a command system in combat but the companions need to be who they are and do what they do best rather then being a lost puppy without any sense of being, just a robot that follows you around for eternity.
It would be cool if as you play through the game you meet potential partners and stay in close contact with them to build up reputation the more you work with them. But these companions don't stay with you. They live their life, do their thing. When you need them for a specific mission, you call them, they'll meet you, you now embark upon the mission ahead. Once completed, the rep you build with them might go up, might go down depending on how much or little they agree or disagree with the actions of the mission.
