I haven't really felt any change in the main storyline.
?!?
I'm only level 8 and noticed already a few "little" changes in the main story flow ... ;-)
Not that "big", but in my opinion good improvements depending the flow, the follow up of the main storyline & you can read in your logbook more details than before EE .
But maybe I'm the only one who find these changes are a good thing Larian Studios did ?