I think if he did appear, it would be like this: The turtles are (for some reason) are taken to an intergalactic prison, and when they break out they accidently release every other prisoner, one of which is Ch'rell. At one point, the Turtles meet Ch'rell. Ch'rell reveals that he was once on Earth and he was the Shredder in feudal Japan and the founder of Foot Clan until he was caught and imprisoned. He eventually uses robotic components to build a robotic shredder body. He also builds some robotic Foot soldiers.
I hope not. 4kidsTV destroyed my love for the franchise with their dumb voice actors, their lack of 'death' and 'killing' (or even not using the words), their lack of Bebop and Rocksteady, their theme music, and Shredder being Krang. Chrell has NO place in the reboot Nick and the series developers have brought into the telavised world! Besides, I like Shredder the way he is, human and vengeful @ Hamato Yoshi!
The CLOSEST you'll get to Chrell is Kraang Subprime. He's got a similar mark on his face, so all we need is for him to team up with Shredder for an episode and show off his villainy. Either that or a 2012 incarnation could be a partner of Lord Dregg. Dregg's always been the best equivalent to Shredder anyway.
With how much the series now seems to be bending over backwards to become more like the 1987 TV series (and even 1987 Krang being brought over), the chances of new references from the 2003 TV series making the cut become scarcer and scarcer. But I've already long since lost faith in this show. (Amazing Adventures #7 was excellent, by the way. :) )