You can test it out, perform whatever combo you like on the both of them and you will get the same damage as a result. I just tested about a few more to make sure and it always seems to be the exact same on both characters.
Did you also try transformations? I know certain characters (if not all them) gain more defensive power when transformed. If there isn’t a ratio between the two then maybe it’s my own reckless in trying to keep Ayame transformed…and I get pound with her more than say wang - tang in trying to take advantage of her speed and finese.
man i love power stone. still play one and two to this day. power stone 2 is the reason i still have my DC hooked up. i use wangtang, falcon, ryoma, accel, and pete.
I hate the flame throwers in Power Stone 1. 
This is the only fighter for some strange reason in all of existance. That I just sucked at. And I will never know why.
Maybe people it has more similarities to old beat em up games than one on one fighters. Power Stone is a very odd game to approach for a person who has been playing fighting games for awhile. Escape system is weird. >.>
I was having good Power Stone matches all weekend and the minute I started recording everything went to shit. I don’t know exactly what happened but we just couldn’t play anymore. I got some good moments from it but barely any. We even started miss every simple stuff, like air grabbing after someone lost Power transformation. I got this shitty Ryoma combo but not much else.
The better option for this would be to let them drop after you hit them 7 or 8 times (forget which). Then when they get up in dizzy status you grab them or perform a Super, this way you will do more damage because the super would not be weakened by the damage dampening done during combos.