Shadows is good, but here's everything I found so far that they removed

Synchronization points no longer clear the fog on the map.

No more torch.

Berries can't be picked up to heal.

Assigning abilities is strict.

No more memory corridors after assassinations.

No more modern storyline.

No meditation to skip time.

No autodrive, horse or boat.

No territory map that showcases all activities.

No bird.