By looking at the following youtube video I notice that some of the polygonal objects have (very simple and primitive) textures in the 3DO version, something the AitD engine on the PC could not do, and the inventory screen is drawn over the game with transparency:
http://www.youtube.com/watch?v=_m612wL1QOI But the visual differences are minor, in my opinion. Gameplay, backgrounds and music seem to be exactly the same.
Edit: After looking again, those are not textures, some models (like the interior of the chest, or the legs of the zombies) are simply redone with more polygons or use a different color which is why they look different.
Edit2: The Playstation version of Alone in the Dark 2 hat texture mapped models (completely redone from what it looks like):
http://www.youtube.com/watch?v=J9BxcgWvGbY