Bowser is an obvious choice. He's always after the power stars in the main Mario games, so it would be natural for him to be the main antagonist in the fan fiction too. He could be more devious than ever, using the power stars to enhance his strength and create new, more difficult challenges for Mario.
Well, a cool plot for Super Mario Power Stars fan fiction could be about a time - traveling adventure. Mario finds a power star that sends him back in time to when the power stars were first created. He has to learn the secrets of their origin in order to stop a new villain who is trying to destroy all the power stars in the present. Also, a story where Luigi accidentally activates a power star in a wrong way and it creates a parallel universe where the roles are reversed, and Mario has to figure out how to get things back to normal.
Another possibility is that a group of Koopa minions could be the main antagonists. They might be under the orders of Bowser, but they have their own little schemes going on. They could target Mario - turned - girl because they think she'll be an easier target in her new form, but they are in for a big surprise when she shows her strength.
Another option could be an evil version of Princess Peach. She could be possessed by some dark force. This would be a very interesting antagonist as Mario and Luigi would be hesitant to fight her at first because of their loyalty to the real Peach. But as she causes more and more chaos, they'd have to find a way to save her and the kingdom without harming her.
Mario is one of the main characters. Also, Bowser who is usually an enemy but in this story is an important part of the adventure. And Geno, a character with unique abilities.
It could be a super intelligent pirate who has been secretly controlling events in the One Piece world. This antagonist might be several steps ahead of everyone, creating elaborate plans to take over the Grand Line. Luffy, with his newfound intelligence, has to match wits with this foe.
The main antagonist could be a mean-spirited mole. This mole is constantly digging tunnels under the garden and causing chaos. He doesn't like Gnomeo and Juliet's love because he believes it's disrupting the natural order of the garden. He tries to separate them by causing misunderstandings between their families.
An organization that believes in using Pokemon for dark magic could be the main bad guy. They see Iris and her Pokemon as a threat to their plans, so they constantly try to stop her. They might have their own powerful, corrupted Pokemon that they use to battle Iris. They could also be stealing Pokemon from other trainers to use in their dark experiments.
It could be a Decepticon who sees the 'Son of the Stars' as a threat to their plans for domination. Maybe a powerful Decepticon leader who fears the special powers that the 'Son of the Stars' might possess.
It could be a rival politician who sees Trump's association with Grimace as a threat. This rival might try to spread false rumors about Grimace being a dangerous or untrustworthy being, just to undermine Trump.
It could be a powerful and corrupt businessman. He saw the potential of the zombie virus for his own gain, like using the zombies as a weapon or slave labor. So he tries to stop Rizzoli and Isles from interfering with his plans.