Okay, not sure how long Gaiamon can stop time; that sounds like a deciding factor. A permanent timestop almost guarantees a stomp unless the other character possesses resistance against it or something. Then again, speed is equalized.
As for everything else though, Samus has an answer to all of Gaiamon's other hax aside from the time manipulation stuff. Samus does have time deceleration, but that's weak compared to time stop. Samus has the Ice Beam, Wave Beam, and Plasma Beam, which are all stacked together with infinite ammo; although, ice beam isn't stacked with them in Samus Returns, but that's more game mechanic purposes. So in canon, Ice Beam is stacked with the Wave Beam and Plasma Beam. Additionally, Samus has a massive area of effect that she can also spam; plus, Wave Beam and Plasma Beam ignore conventional durability. It can bypass nearly all sorts of barriers and armor, and phases through enemies while simultaneously damaging their entire DNA. The combination of those three could freeze Gaiamon's DNA to near AZ temperatures.
Additionally, Samus has great resistance to Mind Manipulation and Life Manipulation, while also possessing Life Manipulation and Energy manipulation herself. Much of the various boss fights involve Samus absorbing the enemies life energy throughout the fight. Samus also has resistance to gravity, extreme heat, near AZ temperatures, electricity, and atomization. Samus also has pre-recognition, but not sure if that quite compares to Nigh-Omniscience, but it would help to predict Gaiamon's moves. Their scanners would also go toe to toe with each other, and Samus has temporary invulnerability with Electric Barrier, Screw Attack, Speed Booster, and Shinespark.
Not sure who to vote, still need to know about Gaiamon's time manipulation stuff, but I'll lean towards Samus for now.
