My experience is that brake feel improves after changing lines and a proper bleed.

There is a process with seating new pads to mate up with the rotors and "cook" a little of the bonding agent out of the pads, but that may mean slightly reduced braking effectiveness and not a spongey feel.

The mechanic is not entirely out to lunch, but a spongy feel and long travel is probably an improper bleed.

Link to TireRack article on seating pads: http://www.tirerack.com/brakes/tech/techpage.jsp?techid=85