Mikey and Leo are the only two that grew up together in this universe, Raph and Donnie were taken as children.
Donnie grew up as somones pet (Hence the collar) & Raph was a lab experiment before he managed to escape. He spent a good chunk of his life with Casey, who's mum altered some of Casey clothes to fit around hs shell.
Raph feels more comfortable in clothes because Casey and him mum treat him as if he was human, and humans don't walk around naked.
Yeah, he had lots of issues in that story. Mikey and Leo are the only two that grew up together in
