Reverse - Flash could be a great antagonist. He could team up with one of Supergirl's foes like Reactron. Reverse - Flash's speed and devious nature combined with Reactron's ability to emit radiation could pose a serious threat to Supergirl and Flash. They would have to figure out how to stop these two villains from causing chaos.
The Dominators could be a great choice as well. These alien invaders could see both Supergirl and Flash as threats to their plans of conquering Earth. They have advanced technology and powerful physical abilities. Supergirl and Flash would need to unite the other heroes on Earth and use their combined powers to fight off the Dominators.
Lex Luthor could also be an antagonist. He could somehow get his hands on some technology that allows him to slow down Flash and nullify some of Supergirl's powers. Luthor's intelligence and his thirst for power would make him a formidable foe. He could create elaborate traps and schemes to try and defeat the two heroes.
Reverse - Flash could be really interesting. He could manipulate time in ways that not only affect Flash but also Supergirl. For example, he could go back in time and prevent Supergirl from arriving on Earth, which would change the whole timeline. Flash would then have to convince her to come to Earth again while also dealing with Reverse - Flash.
Lex Luthor could be a great villain. He might be jealous of Supergirl's powers and see Flash as an obstacle in his plan to defeat her. He could use his scientific knowledge to create some sort of weapon that targets both speedsters and Kryptonians.
One idea could be that a powerful villain from another dimension is causing chaos in both Supergirl's and the Flash's cities. They have to team up, with Supergirl using her strength and flight to combat the villain's minions on a large scale, while the Flash uses his speed to disrupt the villain's energy sources. Maybe they also discover a connection between their powers that helps them defeat the villain in the end.
Another interesting idea is a mind - control situation. A powerful telepath takes control of some of the heroes and villains in their respective cities. Flash, Arrow, and Supergirl have to find a way to break the mind - control. They start by finding the source of the telepath's power. Along the way, they discover that the telepath has a tragic past that led to this misuse of power. They try to reason with the telepath while also fighting off the controlled allies and villains.
One idea could be that a powerful villain threatens both their cities simultaneously. Supergirl and The Flash have to team up, and in the fanfiction, their different powers and personalities could lead to some interesting interactions. For example, Supergirl's strength and The Flash's speed could be combined in unique ways to defeat the villain.
Well, Cisco Ramon from The Flash would be a great addition. He could use his tech skills to create some new gadgets or figure out ways to counter the villains' powers. Also, Martian Manhunter from Supergirl's side. His shape - shifting and telepathic abilities would add a whole new dimension to the story.
In the fanfiction, their teamwork could be shown as a bit chaotic at first. Each hero has their own way of doing things. Arrow is more stealthy and methodical, Flash is impulsive and fast - acting, and Supergirl is more of a straightforward hero. But when they face a really tough enemy, they realize they need to combine their approaches. So Arrow might come up with a plan that incorporates Flash's speed for a quick execution and Supergirl's strength to overpower the enemy's defenses. They would have to communicate constantly and adjust their teamwork as the situation changes.
The Time Trapper would be a great antagonist. He has his own powerful time - related abilities and goals. If he and the Reverse Flash cross paths, they could be in a struggle for control over time itself. Since the Reverse Flash is used to being the one causing chaos with time, having the Time Trapper oppose him would create a lot of interesting power struggles.
In a combined universe, the concept of 'most powerful' can be quite relative. Flash's speed is a huge advantage. He can literally be everywhere at once, save people in an instant, and even time - travel under certain circumstances. Supergirl, on the other hand, has raw power. She can lift heavy objects, fly at high speeds, and has heat vision that can cut through almost anything. Arrow's skills lie in his combat and strategic abilities. He can turn almost any situation into an advantage with his well - placed arrows. But considering all - around power, Flash might be the most powerful. His speed gives him the ability to manipulate time and space, which is a very powerful concept.
If Barry was stabbed, the story would change drastically. His speed is what often saves the day, so without it, the villains would have an upper hand. Supergirl would have to cover more ground and face tougher challenges alone or with less - experienced allies.