Every time brake pads are replaced, even if brake disks are not turned (lathe), the new pads have to "sit" on the disk brake surface. It is normal to feel a soft brake pedal for the first few kms driven.
In fact, several downhill brake "abuse" at this stage, helps new pads sit properly very fast. Sometimes as fast as going back to normal braking the next day. Give it a try. Find youself a medium long downhill road and "abuse" your brakes a few times, but not as hard as to actually "smelling" the brakes. I am sure this will correct the soft pedal feeling.