Personally, I think Mega Man takes this. This is going to be long.
Mega Man is a robot and as such shouldn't be affected by biological abilities or anything that would affect a living being. Mega Man may not have a resistance to them listed specifically on his profile, but we're not going to sit here and argue that abilities like poison or hunger inducement are going to work on a robot are we? Unless proven otherwise, this is a fact and considering that The Hunter has only fought giant monsters, I'm even more inclined to believe that this is true. Also, please don't mention Mega Man's black holes and use it as justification as to why sleep manipulation should work. That is an extremely poor analogy and the legitimacy of his black holes have been discussed several times before. Mega Man's black holes are real and justified - that's final. On that note, Mega Man resists any of The Hunter's abilities that deal with the body, soul or mind since again, he's a robot.
The Hunter's stealth isn't going to be that big of an issue as well considering Mega Man has fought foes who were capable of invisibility, spammed teleportation, and spammed time stop respectively in battle and always came out on top. He even correctly predicted where
Flash Ma was going to appear after a time stop. Mega Man traversed through pitch-black areas and overcame invisible obstacles before in rooms full of spikes. Needless to say, Mega Man's senses and experience in combat should allow him to contend with The Hunter's stealth.
The Hunter has many opportunities to hit Mega Man? Well, so does he. Mega Man has several AoE weapons that just demolish the area like meteor showers, AZ blizzards and other forms of AoE, homing attack and danmaku-like weaponry. He can also slow down and stop time, activate the Double Gear System to speed himself up to the point where time seems slowed down, transmute things into concrete, black holes to suck up projectiles, weapons and his opponent, etc. Mega Man also has access to several forcefields and attack reflection. It seems that The Hunter has no answer for these weapons.
Lastly, Mega Man's intelligence in combat is a huge factor here. His whole strategy centers around adaptation and exploiting weaknesses. Mega Man is resourceful with his weaponry and will notice that if some of his attacks aren't working, he'll switch it up until he finds weapons that do work. Additionally, if he sees that The Hunter is constantly switching up tools and such for different abilities, then who's to say that Mega Man won't forcefully snatch those weapons out of his hands or transmute them into concrete and such?
The only good points for The Hunter are his power null, statistics reduction, probability manipulation and his own resistances to Mega Man's elemental attacks. But even then, The Hunter's power null only seems to work on his elemental attacks, statistics reduction (like Dragon Element) says it saps away strength which may imply it decreases physical strength and not overall AP (correct me if I'm wrong), probability manipulation is vague (since all that's said about it was that it will allow Hunter to land hits on Mega Man and dodge attacks) and needs some elaboration on how it works and while it's good that Hunter resists a good chunk of Mega Man's elemental arsenal, it depends on the armor (so it's not like Hunter can resist everything off the bat unless he can stack armors and stuff) and Mega Man has more weapons in his arsenal than elemental attacks (energy projectiles, shields, space-time manip, attack reflection, sticky explosives, homing attacks, etc).
