There could be a number of reasons.
1. The pedal could have become softer
2. The Drive by wire does away with the direct cable connection between gas pedal and engine, so maybe the drive by wire has made your pedal softer due to "learning". You can try to disconnect the battery for a few hours so the drive by wire will reset and then reteach it by driving hard, but I really don't know if the whole learning thing is true or just BS.
3. If power is what your trying to compare then you should try full throttle tests and compare it that way. Even better try 0-60 times.
4. Another issue could be your break-in process. It's very possible that because you broke it in so gently you have lost power. Read this thread for more info on break-in:
Engine Break-In Techniques