Another option for the main villain in an 'avengers arrow crossover fanfiction' is an interdimensional warlord. He has conquered many other universes already and now has his eyes set on the combined worlds of Arrow and the Avengers. He has an army of powerful creatures from different dimensions. His goal is to steal the unique resources from both universes, like the vibranium from the Avengers' world and the Mirakuru from the Arrow world, to power his own empire.
Maybe it could be a time - traveling criminal. This villain has the ability to jump between different timelines and has noticed that by disrupting the key events in both the Arrow and Avengers universes, he can create chaos and then rule over the resulting mess. He would constantly be one step ahead of the heroes as he could manipulate time to his advantage. He could also use his knowledge of future events to set traps for the Avengers and the Arrow team.
One possible plot could be that Oliver Queen gets transported to the Avengers' universe. He teams up with Hawkeye, sharing their archery skills and combat tactics. They could go on a mission to stop a new threat that combines the technology of the Arrowverse and the super - powered enemies of the Avengers.
Thanos could also be a good option. Imagine Bella's planet holds one of the Infinity Stones that Thanos needs. He would stop at nothing to get it, and Bella and the Avengers would have to join forces to protect it. Thanos' brute strength and strategic mind would pose a huge challenge for them.
A powerful necromancer could be a great main villain. He tries to control the ghostly avengers for his own evil purposes, using dark magic to manipulate them.
One possible plot could be that the Avengers are somehow transported to the Arrow's universe. Maybe a villain in the Arrowverse has acquired a powerful artifact that creates portals, accidentally pulling in the Avengers. Then, they team up with Arrow and his team to fight against a common enemy, like a new super - powered threat that neither group could handle alone.
A possible plot could be that Oliver Queen from Arrow gets transported to the Marvel universe where the Avengers operate. He might initially be seen as a threat, but then he teams up with the Avengers to fight a common enemy. Maybe a villain that has powers related to both the technology in Arrow and the superpowers in the Avengers' world.
It could be Loki. He might have some new trick up his sleeve where he makes the Avengers forget Tony as part of a bigger scheme to cause chaos among the team and weaken their defenses. He could be planning to take over the world while the Avengers are distracted by this strange memory loss.
You can start by looking on fanfiction platforms like Archive of Our Own (AO3) or FanFiction.net. These sites have a large collection of fanfictions. Just search for 'Arrow and Avengers crossover' and you'll get a list of relevant stories. Some might be really good, while others may not be to your taste. It's all about exploring and finding the ones that resonate with you.
The Reverse Flash could be an exciting villain in a Supergirl Arrow crossover. His ability to move at super - speeds would make him a formidable opponent for Supergirl. He could also mess with Arrow's timeline, creating chaos in both their worlds. Imagine him going back in time to prevent Supergirl from arriving on Earth or changing events that led to Arrow becoming a vigilante. His manipulative nature and his connection to the Speed Force would bring a whole new level of complexity to the crossover story.
Ra's al Ghul would be a great choice. He has ties to both the Arrow universe and Batman's world. He could be manipulating events in both Star City and Gotham, forcing Arrow and Batman to team up to stop his grand scheme. His immortality and vast resources would pose a huge challenge for them.
A powerful demon lord from the underworld could be the main villain. This demon lord could be seeking to expand his territory into the Naruto world, using his dark magic and hordes of minions.