I don't think it sucks as much as you think. There's definitely problems, but I think they can be solved by making tweaks to what's there as opposed to completely changing it to be more like the RTS style of BG, Pillars or Eternity, etc.
Everything can be salvaged somehow to some extent, but at some point a wise man has to realize when all the effort is just going on putting more lipstick on a pig.
If you get rid of the headaches of things like stealth, pathing, etc. Then I really don't think it's that bad. I mean this system was basically used in DOS 1 and 2 and tons of people love those games.
Yeah, well... How? By making these things automated improving the auto-follow? This is all a long series of convoluted work-arounds that are simply trying to ignore the core of the problem. The system doesn't work. It's counter-intuitive, cumbersome, slow to use and a waste of time to adapt to.
It's not just that the alternatives are better in some areas. It's that they are better in every single one and the only redeeming feature of the system ("Just control one character if you want, the other will follow") has been done better by other games and can STILL be used passing at other control schemes.