having a way to beat an opponent =/= being able to beat that opponent.
Konohomaru can kill hashirama if hashirama just sits there and lets konohomaru walk up to him and stab him in the head. That doesn't mean Konohomaru > Hashirama.
Even if no one can break shisui's genjutsu, he still has to land it first and that's not happening against people who can kill him with clones, are too fast to be caught, don't have to look at him in order to fight, people that can use edo tensei, people who fight at long range, basically anyone who can beat him before he forces them to make eye contact with him. And that list is extremely large even if shisui had itachi's stats.
