This is just an opinion of mine.
To me it looks like Skyrim scales up to 3-4 cores, but Phenom II isn't fast enough to show much difference.
Higher IPC is better for games mostly due to faster processing of threads, including the graphics dependant threads, which can increase FPS in certain situations.
Just because a core isn't at 100%(registers being full) doesn't mean that it is keeping up with producing frames. Each cpu has its frames limit based on IPC, clockspeed, the game's engine, and the complexity of the scene. Getting the other threads out of the way of the graphics dependent threads will help increase framerates, but there is still a limit.
The Core series being much about 40% higher IPC would make the game about 57fps, if the graphics don't bottleneck, compared to Phenom II X4. It scales really well up to that.