Maybe the reason Urahara gets exiled for creating those untrackable gigai's is this (also my prediction for the end of the minus chapters) :
After Urahara fixes up the vaizards with the hougyaku (possibly with Aizen watching/walking in, which is how he finds out about it) the vaizards get found out, and SS condemns them traitors/criminals, and thus try to capture them. Urahara helps them escape by giving them the gigais he created, thus making them untrackable and able to completely escape from SS.
Also I truly doubt that Isshin will appear anytime soon, unless simply at the end he's introduced as a new captain. One reason is that he didn't lose his shinigami powers until 20 years ago. The main reason that I just remembered is that Urahara asks Isshin what he knows about the vaizards. Isshin says "A group of shinigami that obtained hollow powers through forbidden methods". That doesn't scream "I know the vaizards are goodies really!" to me. If he knew about what happened I doubt he would've described it as "forbidden methods", it seemed like he didn't know anything about it, except possibly what SS has told him.