Did you only install new pads? Pads wear down the rotor over time and create a thumbprint on the rotor (wear pattern) which is unique to the pad. New pads will not have the same fit subtleties as the old and hence you will have less contact area and braking power. It'd be like trying to put your foot in someone else's footprint..
You should always replace pads and rotors together, but if you don't, there are a couple options; Over time, your new pads will "seat" to the rotor shape and braking will improve, but it may take a while. Another option (if you don't want to replace rotors) is to have your rotors re-surfaced. This is also refereed to as "cutting rotors" and will be done with a brake lathe. This, however, requires that there is decent life left in the rotors.
I have friend in the industry that takes it to another level. He says that even when the rotors and pads are replaced together and are brand new, the rotors should still be cut true to the hub with a brake lathe. This ensures peak performance, but is not entirely necessary in my opinion.
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