What did he do with him exactly? Made him a teenage mutant ninja turtle with no personality. A spoiled brat that constantly lashed out. Been there done that. Everything, He and Dick would start to get close, it was like Morrison thought: Oh hell no! I'm not sure he was even really in Batman Inc. all that much until the end.
That said, the best thing Morrison did was kill him. There was a tad bit emotion there.
Don't get me wrong, I'm glad Morrison created the character, but I don't think he "owned" him in the way Frank Miller "owned" DD even though Stan Lee created him.
Just my two cents. I did enjoy Batman and Robin and Batman Inc.
I just think Tomasi did a better job writing him.