So at the time he was the only living uchiha with mangekyo, he goes to use it on the uchiha to stop the coup and fails while also getting his eye ganked by danzou.... Idk I was really expecting shisui to be kinda badass seeing as he unlocked mangekyo so young but turns out he was a pretty big failure.
We know that Kotoamatsukami requires a huge amount of chakra, and we know that it cannot be used often because it requires a huge amount of time to recharge. Plus, if you can only use it every ten years, then Shusui must have only used it once. If he used it once and did not have enough practice or did it incorrectly or missed and targeted the wrong person (or whatever the scenario is) he would have been weakened enough for Danzo to take the eye.
Plus, we know that Danzo was pretty darn strong by himself, and he was surrounded by other powerful root members (Remember Orochimaru?). He had seals that could immobilize a person, and we know that Shisui was a member of ANBU and would have been in contact with Danzo.
People think that Danzo is a wimp and he isn't. Especially not when he was younger. We know Hiruzen was weaker as he got old and Danzo would have been the same way. 10 years before he died, he might have been much more powerful.