I concur with the points the OP raised. (Better late than never:P)
The auto-follow can result in situations in the current iterration of the game where half your party is jumping around in tight places like crazy.
The links between party members are tedious to handle. Whenever you want to set up an ambush, or just move a single character around, you have to break the party apart one by one, and then reattach everyone afterwards. The only reason this system was tolerable to me in DOS1, and DOS2 was that I've played lone wolf playthroughs. This is probably part of the reason we won't get a larger party, as managing a party of six would quickly become bothersome.
Don't know how time consuming, or at all feasable it would be to change the party control system to something akin to the ones seen in BG, or any of it's spiritual successors, but I think most fans of the original title would prefer the classic control scheme.