The basic controls are the same, but there are a few tweaks in the gameplay. You can save your progress and revisit levels (including Dr. Wily ones), the weapon system has some changes, and the Item-1 and Item-3 are written off.
- Adapted Out: Items 1 and 3 are absent. Mega Man only has an Item similar to the Item-2.
- Antepiece The robot master stages prepare the player to a gimmick before progressively making it harder and dropping it.
- Balance Buff: To compensate for the criticisms to the unbalanced and nearly useless weapons system of Mega Man 2, most weapons were tweaked.
- The Bubble Lead can damage most enemies and it is much more powerful.
- Atomic Fire now has a fire orb in the hand while it is being charged. This buff was an inspiration to the Mega Maker version of that weapon.
- Leaf Shield now blocks projectiles and can be carried for all a screen. It is now tossed with the fire key.
- Time Stopper can be interrupted to avoid unnecesary waste and to get better use to the weapon.
- Crash Bomb explodes in contact to enemies and by volition of the player.
- Nerf: The original Metal Blade was regarded as too overpowered. Here, it can no longer be fired upwards nor downwards, and there can only be two blades at the time.
- Pragmatic Adaptation: To emulate better the limitations of Atari, some level objects were changed. Instead of the Crash Lifts, there are moving platforms moving from left to right and with a pointer that spins from time to time and hurts. The Air Cheriots do not have a circular trajectory, but are moved through shots from the opposite direction Mega Man is standing on them and are separate from Kaminari Goros. Another important change is that there are no continuous screens. The Atari controls were overlooked in favor of an accessible gameplay.
- Retraux: The game is an adaptation of a NES game into an Atari game. Thus the graphics are simpler than those of the original game.