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I think an issue that could have been solved is that Ch'rell could have been killed at TCRI, and the spirit of the Tengu Shredder reanimated the body and wore it as a host as a kind of vengeance for the stolen identity.
At that point, Ch'rell could have been the flawed Shredder who felt that he'd been treated with great injustice his entire life, while Tengu Shredder was just the "Bleh bleh bleh, must take over the things, because I'm evil!!" category that dragged down Ch'rell's capability as an interesting, flawed and possibly even tragic antagonist.
So the entire time, Ch'rell would have been dead, but Tengu Shredder would have played the part of "Ch'rell" so well that no one was the wiser, including his own daughter, that is until things slowly start to get a little bit "off". Skip out on Ch'rell trying to return to space completely. The Utroms could come back initially to collect Leatherhead, but stay to help with the Tengu Shredder problem once it arises (and being the first to notice that something really weird was going on with "Ch'rell") and help Karai learn her father's history with a new perspective. She learns about how Mortu and Ch'rell had once been friends, how Ch'rell ultimately had to resort to being a criminal to survive, how he came to hate his people.
Some enormous possibilities were missed with Ch'rell, and one of them was addressing that he was not spiritually at peace; freeing his body of the Tengu Shredder was one aspect of peace. This would also mean Karai learning the truth of his history and reexamining her sense of honor in a different direction than Leo wanted her to, then using that refound honor to bring peace to her father.
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