The only problem with having Yamamoto as the villain is that Aizen stronger than Yamamato if I'm not mistaken. Aizen hit the limits of everything, while I don't think Yamamoto has yet. So that would mean that fighting Yamamoto would be weak. Once they are finished with Aizen, Ichigo will have beat him marking him as the strongest person in all and any realms pretty much. Unless Ichigo does not beat Aizen. But even still with his Vizard, Hollow Mask it makes him a superior force to all of the captains who are just normal Shinigami. It would hardly be a challenge, unless Yamamoto ends up finding some power that increases a shinigami's strength beyond the preset limits that are attainable.

I can see the whole execution of Ichigo being something valid, but it is also too much of a canon arc since it is going to significantly impact a lot of events. It will end up with Yamamoto in a different position of power at the end if not dead along with whoever stands in the way. There would have to be a number of changes that would impact the original manga story's future too much.

As you said it needs to be something non-consequential to the story. If it was removed it would not change anything. As I understand it, for some reason Ichigo loses his Bankai for a while in the Bount arc. Which ends up making him a more level fighter. So something like that might have to happen with Ichigo again, lame yes. But Ichigo with his mask is insane, even if it is only for 11 seconds. And that amount of time is only bound to increase as Ichigo is more used to using the powers of the hollow.

It needs to be made up almost completely from scratch so that it ends up not having heavy connections to the canon. It could be something related to Urahara again, he has a lot of black boxes. Or maybe Mayuri, who no doubt made a lot of mistakes. Or you could have normal humans developing powers, like Chad and Orihime. Maybe a technology that Urahara invented that removes the hollow part of the soul, and materializes it. So you end up with hollow and shinigami of the same soul but two bodies. And that is how Ichigo loses his hollow powers.