You guys make some damn good points. It's definitely true that BG2, both SoA and ToB felt pretty linear from start to finish, the only real exception being the part after escaping from Irenicus at the start. They always had the dreaded "I hope I didn't forget anything, because I won't be able to come back for quite a while" part that I cannot stand in games.
On an unrelated note, I would be so happy if they worked in your BG1 end-game group into the start of SoA. For various plot reasons they can't really do this (first one that comes to mind would be Quayle somehow being the ringleader of a circus while accompanying you somehow), but I still think it would be pretty cool.
Oh, and a way more obvious conflict would be if you didn't have Imoen at the end of BG1... How was that not the first thing I thought of?