I've always been under the impression that Samus requires much more space to manuver than Megaman. The key is that Megaman, with his charges and different arrays of powers would have much more flexibility in attacking. While Samus's powerbombs would propose a tremondous problems, samus would find it hard to deal with the sheer array of powers that Megaman would have retaining half of all of the Boss powers (which at this point is 24).
For me, the clincher is that Samus has obscene amounts of energy reserves. If Samus had anywhere near the amount of reserve tanks and energy tanks that she had for battling motherbrain, it'd be the equivalent of a boss in MegamanX having 6 energy bars. Heh.