Shisui was a part of Root. We should all know by now that Danzo messes with his subordinates' bodies so that if they ever betrayed him or the organization they would be silenced and killed. Shisui probably had no choice but to let Danzo take his eye tbh. Also Danzo is fairly powerful himself. Btw he was also known for his great shunshin speed.
Also the 3rd Raikage was obviously extremely powerful since he was able to take on and defeat the second strongest biju alone, and only collapsing because he stabbed himself. I don't have any definite proof, but it's safe to say that Gyuki used TBBs against the 3rd, which he could counter (or even tank since his defense is hyped as being absolute, we also saw him tank a FRS at point blank range which attacks at a cellular level -- with minimal damage done). They were definitely strong shinobi