I'm no expert on this, but I did a rotor/pad replacement on an older '75 450SE (no ABS) years ago and the pedal felt like you describe, right after I buttoned everything back up. I went into a panic, concluded I'd pushed the cup seals in the master cylinder backward or something equally stupid when I clamped the caliper pistons in to make room for the new pads. I changed the master cylinder for one I had laying around, bled everything, and guess what - same damn thing!
I talked to a MB mechanic friend of mine and he told me that the new pads/rotors need to seat themselves before that nice hard pedal feel comes back. He told me to just use the brakes for awhile and see if the situation clears itself up. Lo and behold, it did.

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1986 560SL
2002 Toyota Camry
1993 Lexus