Nunleft, there are always options. Straight up talking to him might work, and may be the only long term solution. It sounds like the problem there is that you don't like confrontation. Feel free to show this thread to one of your other players, who might be better suited to that conversation. It does not need to be you.
But there are always other options. I have been messing with this idea for a while.
Create a storyline, and play out the fights. Instead of random generating everything, very specifically create a storyline of encounters, reasons for the encounters, and results of victory and loss. This is a comic book game, and comic books have story arcs, so creat them and play them. Because this can encapsulate the introduction of new characters through story, everyone will be limited to specific decks to start. Since we can have everyone fighting in different places at the same time, the choices of who to play can be restricted. Scholar can defend Tomb of Anubis with Ra against Gloomweaver or help Wraith who has been attacked by Ambuscade in Rook City, but since they are on the other side of the world, he can't do both fights. Scholar has a back story, and that can be used. He stays out as much as possible, which can be incorporated into the storyline. Just as Wriath can have family commitments that makes her unavailable, and Bunker can be called on by the US Army to deal with something they need (they pay his rent after all), or Tachyon has a conference on particle physics to attend, everyone should have times they are not available for some fights. Scholar is written so that he needs a reason to fight.
Series 1: Baron Blade vs. Hero Team. (The Hero team does not need to be the game's Freedom Five. We can create any starting team we want. And it is far easier to inrtoduce some of the FF as part of storyline. Your team would need to start with one deck per player. All other decks become available as storyline progreesses.) Begins in Megalopolis. Then MDP to hack the computers for information about where BB's base is. Then the heroes take him on in Insula Primalis to find his home base, which explodes but there's no way the Baron could survive that...
Series 2: Heroes hear about vigilante leaving caught criminals in Rook City, across the river from Megalopolis. Come to Wraith's rescue when she has tracked down Spite. Beating him reveals he was hired, but by whom. Explosion at Pike Industries, out comes Plague Rat. With victory, same team must immediately fight Akash'bhuta at Pike, who was summoned by the damage to the environment. Investigations taking investigators nowhere. A shot fired at Megalopolis youngest and latest recruit Unity reveals Ambuscade has been hired to wipe out the Freedom team one by one. Spite escapes and needs to be fought in Megalopolis, inspiring Bunker to work with tachyon and Unity to create the Block. They want bots to guard the prison, but their AI goes wrong. enter a series of fights against Omnitron, where some small piece of him keeps escaping and recreating itself. One can be Cairo and the awakening of Ra, the Ennead, and a dust up at Tomb of Anubis. Parse created. Omnitron is ultimately defeated, the Block guarded by humans. Heroes return from a long series of fights to find the criminals overtly in charge of Rook City. They get down to serious business and try to clean up Rook City, leading them to the rumored Chairman that runs organized crime in Rook City. You can have Plague Rat, Ambuscade, and Spite hired to attack Megalopolis and Freedom Tower.
Series 3: Tempest arrives on a ship that crashes, and forewarns the coming of Grand Warlord Voss. Rescue the astronauts at Wanger Mars Base from Voss' scouting force. then face his army in Megalopolis and Rook City. But Voss keeps coming with an entire Intergalactic Empire's forces. Need a defense. Atlantis had one, says the Scholar. Head to Atlantis and face the imprisoned nightmare that destroyed it -- Gloomweaver -- and Nightmist is either created or released. In Atlantis, find no defense, but a teleporter that can take you to one place... choose DokThorath Capital. Influence the Civil War to pull Voss back from Earth to become embroiled in restoring his empire. Only to come back and find Citizen Dawn has set herself up in Megalopolis, with Expatriate there trying to stop her mother alone.
Series 4: Broken timeline and dimensions. Vvisionary breaks down the dimensional barrier to save herself in a parallel universe. Chrono-ranger, Omnitron-X introduced. Environments Realm of Discord, Time Cataclysm, Final Wasteland, Silver Gulch. Enemies La Capitan, Gloomweaver, Dreamer, Iron Legacy. You could set this up as a series of fights against Visionary forms, with Visionary switching through various promo cards to be lighter or darker versions of herself. Introduce the idea that the Matriarch is Visionary, too, gone mad, and using her Psychics to control birds at the end of earth (Final Wasteland), who gets sucked into the original timeline to pester the heroes later.
That's the kind of thing you can do. Present it to the problem player as a greater challenge, rather than any kind of play style issue on his part. "If you're a good player, you don't need the Scholar to win against Baron Blade. Overkill, isn't it? We've got Legacy, Bunker, Haka, AZ, and Fanatic in town, so who would be the best suited for this?"