Both guys lost their legs but at different points in their career. Frank built his striking game before his legs were gone, Ken fought a lot after he couldn't wrestle as wewl, and tried to box with guys, not to mention he was old as hell.
Ken ruined his body in WWF, and abused steroids. Frank mentioned this in an interview and said Ken's problem was he lost his psyche without roids. A pre WWF Ken, healthy and young, was almost superhumanly strong and unstoppable onothe ground according Mikey Burnett.
I think Ken's ego inflated and he stopped working on his game, got used to easily grappling the shit out of people in Pancrase. While Frank brought one or the first true well rounded game plans to MMA with insane cardio.
Frank also got his ass seriously kicked by prime Ken at the Lion's Den, so in a way, Ken made Frank what he was.