The game features a graphical overhaul with 3D character models in a chibi-style and updated environments.
Two new Robot Masters, Time Man and Oil Man, have been added to the game, bringing the total number of Robot Masters up to the traditional eight instead of six.
To fit the two new Robot Masters into the cycle, the entire weakness order has been redone and no longer follows the original game. For example, Elec Man is weak to the Oil Slider instead of the Rolling Cutter. Fire Man and Cut Man are the only Robot Masters to keep their original weaknesses.
A difficulty selection is available, with the options being Easy, Normal, and Hard. The setting changes the player's health and damage, and Easy mode also makes certain platforming sections easier.
The player can play as all eight Robot Masters from the game, as well as Mega Man, Roll (downloadable), and Proto Man (unlockable and downloadable). The Robot Masters are unlocked by defeating them with the Mega Buster. They can also be used to complete certain character-specific Challenges and levels in Story Mode. When the player uses a Robot Master to play a level that the Robot Master originally resided in, they will fight "Mega Man?" instead.
There are 100 new challenges, ten for each of the nine playable characters (Roll and Proto Man do not have their own challenges) and ten boss rush challenges, which involve beating some or all of the bosses in one run. They are mostly very short, but most of them are brutally challenging. Completing all 100 will unlock Proto Man as a playable character in Story Mode.
There are two modes that are available to play: New Style and Old Style. New Style gives the player the chance to play as all of the eight Robot Masters and features level design changes (in order to utilize the PlayStation Portable's wide-screen display) as well as music remixes. Old Style is nearly identical to the original Mega Man, but the super-deformed graphics are still in place, and Time Man and Oil Man are not available to fight against.
A level construction mode is available for players to build their own Mega Man levels.
An online mode is also available for players to upload and download custom-built levels. The player also has the choice to download both Roll and Proto Man from the online mode.
Much like Mega Man 7, 8, and 10, each boss has their own unique entrance. For example, Elec Man comes from a lightning bolt that shoots from the sky, and Ice Man appears from a large chunk of ice that is suddenly created out of thin air.
In another reference to Mega Man 7, 8, and 10 each boss has a special attack, which they only use when their health falls below half of the maximum. In this state, they are temporarily invincible whilst they unleash their attack. They only use this attack when the difficulty is set to Normal or Hard, however.
An exception to this is Time Man, who uses his Time Slow on all three difficulty levels.
Unlike the original Mega Man, weapon projectiles cannot pass through walls.
The game has the largest playable cast in the franchise, which includes Mega Man (plus his three alternate forms), Roll, Proto Man, and the eight Robot Masters. This brings the total of playable characters to fourteen.
Strangely, Proto Man states that he has an unstable nuclear core. In the first few games, he had an unstable solar core, and Doctor Wily doesn't seem to be aware of Proto Man's existence, while he took Proto Man in, again, within the first few games, making this game have quite a few plotholes. However, Proto Man's story is non-canon and is more of a bonus "what-if"-type scenario.
This game had a reputation for selling very low in America, noted by Electronic Gaming Monthly.
Along with low sales, the game has been on Electronic Gaming Monthly's "Japan Issue" on a top 10 list of where Japan went wrong, with Oil Man as a "racist stereotype" type of character.
Mega Man's bio in the instruction booklet mentions that he likes animals, especially dogs. This is a possible nod to Rush.