hey, is there any chance that you're thinking of
Twinsen's Odyssey, AKA Little Big Adventure 2? I woke up after a few hours of uncomfortable sleep with
a full bladder the notion that you might be talking about this classic.
The game was a mix of polygons against pre-rendered isometric for inside areas (like the original game) and a fully 3D world for outside areas (with an odd camera system that could be a bit unpredictable). Like the original game, you get a "Proto-Pack", which at first can only let you move horizontally. Oh yeah, and the game is kind of alien (although the plot of the game features aliens visiting the already rather unusual inhabitants of a world).
If it isn't this game, can you say how the isometric screenshots compare to the game from your memory?