Gwen could be a great addition. She could be the voice of reason when Ben and Vilgax are at odds or she could have her own powers play a role in the story. Grandpa Max is also a good choice. His wisdom and experience could add depth to the fanfiction, especially when dealing with Vilgax. Another character could be Kevin. His ability to absorb energy could create some interesting interactions with Vilgax and also provide a different kind of friendship or rivalry dynamic with Ben.
Power struggle is a common theme. Vilgax is always after more power and often clashes with Ben or other powerful beings in the fanfics. Another theme is revenge. Since Vilgax has been defeated by Ben many times, he often seeks revenge in these stories.
One popular 'Ben 10 Vilgax fanfic' could be 'Vilgax's Redemption'. It shows a different side of Vilgax where he tries to change his ways. Another one might be 'Vilgax vs. the New Aliens' which has some great action scenes with Vilgax facing off against newly introduced aliens in the Ben 10 universe.
Well, a plot could be that Vilgax gets amnesia and Ben has to decide whether to take advantage of this or help him. This could lead to a whole new dynamic between them as Ben tries to figure out what to do. Also, a fanfiction could explore what would happen if Vilgax became a mentor to Ben in a strange, alternate universe. They could train together and Vilgax could pass on some of his knowledge, but also try to manipulate Ben for his own ends. Or, perhaps a story where Vilgax and Ben are both stranded on a strange planet and have to work together to survive, all while dealing with their mutual distrust.
One idea could be exploring an alternate universe where Ben gets the Omnitrix at a much younger age and has to learn to control it while dealing with school bullies who are after his power. Another could be a story where the Omnitrix malfunctions and starts giving Ben alien forms that are hybrids of different aliens he already has access to.
Gwen is an obvious choice. She can bring her magic skills and her relationship with Ben to the story. Also, Grandpa Max, who has a lot of knowledge and experience that can be useful in the fanfic. Another good character could be Kevin, with his ability to absorb materials and his complex relationship with Ben.
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It's hard to say for sure. Vilgax is powerful, but the characters on Comic Vine are diverse and have their own unique abilities. It really depends on the specific match-up.