I've hunted down a lot of Genius Ben fics over the years, and honestly, the ones that stick with me aren't always the most epic cosmic battles. There's a quiet little two-shot called 'Causality Quotient' on AO3 that nails the voice. It's set after the original series, with Ben tinkering in his garage on a Sunday, and the author gets the scientific curiosity mixed with his inherent compassion so right. He's not just a cold intellect; he's trying to solve problems like Plumber logistics and alien refugee housing. The prose is methodical but warm.
Another standout is the longer crossover with 'Young Justice', 'Omnitrix: Cognitive Anomaly'. This Ben enters the YJ universe with his intellect already amplified, treating the League's problems like complex equations. The dynamic with Batman is less about rivalry and more about two vastly different methodologies clashing—Batman's contingency planning versus Ben's adaptive, real-time solution generation. It does a great job showing the emotional toll, too; his friendships with the Team strain because he sometimes talks like he's debugging their interpersonal conflicts.
For something completely different, there's a hilarious crack-treated-seriously fic on FFN where Genius Ben gets dumped into the world of 'Phineas and Ferb'. The entire plot revolves around him and the boys trying to one-up each other's inventions, with Doofenshmirtz mistaking Ben for a rival 'evil scientist'. It's pure, joyful chaos and a refreshing take that doesn't take the concept too seriously.