There are some subtle changes, you should have noticed at least one of them
The intro video starts differently. With the expansion it starts with a new character giving info to central that triggers the video that leads into the first tutorial mission (where you rescue the commander).
If you did the tutorial (again) your not forced into building a specific facility in a specific spot.
If you do the mission to secure the power core (again think this is tutorial), it has a new more atmospheric map.
If you disabled the generic tutorial options but kept the WoTC tutorial option enabled at some point you will get to do the new WoTC tutorial mission that introduces lots of new stuff. I "think" this is automaticaly triggered as the next mission after you blow up the monument, but its possible there were other missions in between. (not many if there were).
The difference between vanilla and expansion is like the difference between the TV edit of LOTR and the extended directors cut. Its the same film mostly just with lots of extra stuff squashed in. It still starts in the shire and ends with a ring in lava.