I like NPCs that are controlled and equipped by me, but feel like they have their own personality and agenda. I think it adds a lot of depth and immersion when characters with very different views from me choose not to continue journeying with me, but tactically, I like being able to switch to them when necessary.
That being said, I could be persuaded to allow them to be autonomous. Fallout: New Vegas had excellent companion design, but again, that's mostly because the characters had their own back stories and agendas, and wouldn't go along with someone who did what they didn't believe in.