this is my take on who isshin is...
Isshin is an old shinigami captain... he maybe was urahara's predecessor. He also may have helped Urahara and the Vizards move to the real world. That's why he can't return to the Soul Society same as them.
He may have lost his shinigami powers because Urahara gave him a special gigai like rukia's. It was a gigai that eats the spiritual energy of the shinigami thus making him/her human. Therefore, he may have been helping urahara hide the hogyoku before rukia came. That may also explain why Isshin regained his powers back when urahara gave rukia the speial gigai and gave isshin a normal gigai instead.
I also agree with the possibility that Isshin's wife, Masaki, is a relative of Ryuken Ishida. That's why they know each other. They never intended to let Uryu and Ichigo know because of the quincy-shinigami conflict.
Sorry if these have been mentioned in previous posts...
