Iirc, Beast in all three movies showed physical superiority to Cap. Jumping dozens of feet casually, turning into a human pinball, circling the entirety of the mansion at low level superspeed, etc...
Beast wins some matches due to being physically better than Cap, but Cap's mix of powers and skill nets him wins as well. Probably a few more due to Beast having almost no skill to speak of aside from natural talent.
While I like Cap more, I think Beast has this. A lot people think that Logan would give Cap a good fight and has the potential to beat him. And a young Beast was manhandling Logan with seemingly minimal effort, and seemed at least equal, if not superior, to Cap with regards to physical stats. Now some could say that Logan wasn't in full on battle mode, but I doubt he would have let Beast toss him around if he could have prevented it. Add in decades of experience leading up to X3, as well as a noticeable increase in bulk/muscle, and Beast should take this one.