Working properly,stock brakes should throw you over the bars.Make sure your pin is cleaned and lubed and more importantly,both slides.Also,remove the chrome isolators from where the pads sit and clean(sandpaper) those as well as where they sit in the caliper.Silicon brake grease these contact points as well.If your pads bind at all for any of the above reasons,you will have crappy brakes.Never just tip the caliper up and slide in new pads when it's replacement time.As stated above,replace your fluid evey year as it's hygroscopic(attracts moisture)
Having said all that,if your brakes were better before you replaced them,that's more than likely because your rotor is worn more at the outer circumference(thinner) than the inner.When this is the case,the old pads will have worn tapered.Without replacing the rotor,the brakes won't be as strong and will be spongy until your new pads wear tapered to match the rotor.
That's the sole reason for KTM's cauliflower style rotors.Having only part of the outside circumference of the rotor contact the pads equalizes the swept area with the inside circumference allowing your pads to wear evenly.This is that styles sole purpose.They aren't better brakes but will be when you replace pads just because they are worn even.
