As Samus is my secondary I can give you a couple tips about the matchup:
Zair is your best friend and it outranges Megaman's projectiles and aerials exept for metal blade. You need to alternate offense and defense using the best neutral game tools which are Nair, Zair, first hit of jab, shielding and jumping backwards to Zair again. You have to find an opening for a dash attack abusing of some landing lags like his Fair or Bair, or Nair/Jab endlag or by hitting a landing Zair to connect into dash attack upair and any followup you get reacting to his DI. Bombs can also help you at microspacing while you can use Super Missile to shield pressure if he has a low shield and charge a shot to force an approaching if he tries to play a bit stallish. The matchup is not bad at all, but you need to space yourself correctly to be safe from his aerials while you can instead hit him with Zair or other things