So, while Kyubey didn't know the specifics of Madoka's karmic blessing before the last few episodes, he definitely seems able to gauge her massive potential and is aware that magical girls are not created equal.
Late timeline Madoka is obviously stronger than all predecessors by a longshot, seeing as the world would be gone if previous witches could be planetary threats like hers. Still, her potential was more or less artificially boosted by Homura's timetravel. Kyubey already understanding that some girls have the ability for greater wishes and stronger magic implies that there have been girls who naturally had more potential.
I wonder why a girl would naturally have more potential though? Would she just produce more energy through stronger emotion? Or maybe she would have had to have done great things to change history before making the wish? (like Joan of Arc already accomplishing alot on her own and THEN making a contract)