I think two things should be done. Not necessarilly in the same game, but as two different ways of doing it depending upon the kind of experience developers want to give.
1) Increasing strategy.
2) Increasing independence.
1) If they want us to maintain strategic control over companions, we should be able to have some strategic control both in and out of combat. Including being able to plan who carries out what out of combat tasks and perhaps how they do it, such as who engages in conversations and at least some influence in how they engage.
2) Full control of companions is something that BG2 had not just because it was designed that way but because the nature of AI at the time, it couldn't really have been designed any other way. NPCs couldn't be trusted to behave intelligently. As computers become more powerful, AI can become more intelligent. Companions can start becoming more in control of their own actions without ****ing the player over. The player, as party leader, can assign roles and give basic outlines of tactics and strategy but its up to the AI to choose if and how to carry it out. This may seem a horrible idea simply because its relatively new and it seems to take away control from a player in comparison to the IE days. However, it encourages respect for the independence of AI characters and attachment to your own character. It can also have some interesting interactive consequences.