Hi,
The 3GS gpu performs much better than the iPhone4 GPU (same gpu, 4x more pixels). When optimizing, make sure you check on iPhone4 instead of 3GS for performance bottlenecks.
The 2 shaders should mostly perform the same, but... the key bottleneck there is going to be the fact that they are transparent. Solid shaders perform so much better on the PVR architecture its not even funny. If you have a lot of solid textures, its probably better to change the material on them - you'd get much bigger gains like that (at the cost of CPU overhead for draw calls)
Cheers,
unikron
p.s. iPhone 3G is a different beast altogether, and the performance is quite a bit worse than 3GS.