As someone who almost exclusively used Revit for renovation and other existing building projects, the fact that new and existing walls automatically join is maddening. There is rarely a time when you want this to happen. The API should be changed so that elements created on different phases are automatically disjoined from each other, with the option to join if desired, not the other way around as it is now.
So many people complain that Revit is not good for existing buildings. Changing this would help toward getting rid of that general perception.