Characters on Mega Man's side
Nick Fury, Mega Man, Proto Man, Eddie, Rush, Darci Roll, Supergirl, Black Panther, Wolverine, Storm, Shadowcat, Rogue, Professor X, Ice Guy, Phoenix/Jean Grey, Beast, Cyclops, Angel, Nightcrawler, Mr. Fantastic, Invisible Woman, Harley Quinn, Deadpool, Cat Woman, The Thing, Human Torch, Spider-Man, Iron Man, War Machine, The Penguin, Cyborg, Captain America, Batman, Black Canary, Robin, Black Widow, Hawkeye, Lex Luthor and Mercy Graves
Neutral
Callisto, Pyro, Magneto, Lady Deathstrike, Dr. Doom, Electro, Green Goblin, Dr. Octopus and Bane
Characters on Wily's side
Dr Wily, Bass, Treble, Concrete Man, Galaxy Man, Jewel Man, Plug Man, Tornado Man, Magma Man, Hornet Man, Splash Woman, Big Stompers, Shield Tankbots (in NES-version of Mega Man 9 called for a "Kakinbatank"), Mega Mech Sharkbot and Police Man (in the NES-version of Mega Man 9 called for "Fake Man")
Three Main differences of this title
Wily is not trying to trap Mega Man in the same way as NES-version.
Plus these robots (including the robot masters) were created by Wily. Dr Wily didn't threatened those robots to be destroyed.
Mega Man is still able to slide and has chargeable Mega buster, even in Mega Man 10.
Prior to Mega Man 9 (between 2nd title of Mega Man 8 and first of Mega Man 9)
Now it is the year 2072, from after fall of Kingbot, Decepticons and Wily's defeat, Mega Man and his hero comrades seen peace return again. People began to forget about Wily.
Mega Man 9: Ambition's Revival (15th June 2073) (About a year after Wily's last defeat)
However, nearly a year later, 2073, new robot masters, a giant robot boss and robo mini-bosses attacks Metropolis again. Those new robot masters are Concrete Man, Tornado Man, Splash Woman, Plug Man, Jewel Man, Hornet Man, Magma Man, Galaxy Man and Police Man, while the other robots are Big Stompers, Shield Tankbots and Mega Mech Sharkbot. Those robots are currently led by Bass. But Wily blames Lex Luthor and Mercy Graves for being behind those robots this time, which soon became apparent that these robots were those created by LexCorp. Dr. Wily interrupted all television programs to announce that these robotic riots were not his doing. He then continued to show video evidence that proved LexCorp's involvement in the recent violent outbreaks. To make matters worse, Wily gave the account number to his personal bank account and announced that he would accept donations to build his own robot army to counter that of LexCorp's or Nick Fury's. Mega Man (also by clearing Nick Fury's name) along with his hero comrades returns to see the proof.
First Iron Man, Angel and War Machine meets Hornet Man, Tornado Man and Galaxy Man. Then those heroes quickly defeats those first three robot masters.
After defeating those first robot masters, Invisible Woman, Storm, Rogue, Spider-Man and Human Torch meets four Big Stompers and three Shield Tankbots.
After defeating those robots, Angel and Iron Man confronts and defeats Concrete Man.
After defeating Concrete Man, Mega Man confronts and defeats Plug Man.
After defeating Plug Man, The Thing, Black Canary, Supergirl, Black Panther and The Penguin meets three Big Stompers and two Shield Tankbots. Then the heroes defeats those robots.
Later, Ice Guy, Invisible Woman, Harley Quinn and Proto Man meets Jewel Man and Magma Man. Then the heroes defeats those robot masters.
After defeating those robot masters, Iron Man and War Machine decides to find Splash Woman. First Iron Man and War Machine talks to her, and even begging her to give the proof. But she refuses and challenging them for fight. The fight is long, but in last they're defeating Splash Woman.
After defeating Splash Woman, Iron Man brings one of the robot's internal memory units to Nick Fury for investigation. As it turned out,these robots are created by Dr Wily, not LexCorp. They were sent fake as LexCorp's robots, to see LexCorp as the heroes opponent, not Wily as theirs.
When the heroes knows that Wily is the antagonist, they're returning back to Metropolis to defeat some more robots. First the heroes together defeats Mega Mech Sharkbot, then they're also defeating ten Big Stompers and ten Shield Tankbots.
After defeating those robots, Wolverine, Cyborg and Proto Man confronts and defeats Police Man. A moment later, Proto Man meets Bass, then confronts and defeats Bass. Wily gives up for today...
To be continued...