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http://static.comicvine.com/uploads/original/11113/111131174/3349683-.tmnt.jpg

The Mirage comics TMNTs.

VS

http://static.comicvine.com/uploads/original/14/144096/3842198-5445783375-idw-p.jpg

The IDW comics Shredder.

Mirage.

Leo himself could probably win, considering he defeated an uber Shredder created from some kind of worms that constantly regenerated. And his skills are good enough to keep up with Miyamoto Usagi, which is a canon crossover.

Add in Raph, who beat Leo in a physical fight, and the other two, and it becomes a stomp.

Shredder wins. Just because th Mirage version could come back to life when he dies, that doesn't make him better than the IDW version. The fact of the matter being that the IDW version doesn't die every time he appears in a comic should be reason enough for why he wins this but when you look at some of his feats, it quickly becomes apparent why he's still alive and why he's the toughest guy in the entire comic.

^ his fight with krang alone is proof enough of that, imho.

Shredder wouldn't last against the likes of Usagi. (If you don't know who he is, look up Stan Sakai, the creator. Guys a living legend.)

Mirage turtles are also a good deal tougher then other versions. Casey Jones spent an entire issue just beating on Raph with various weapons, and all he did was wear himself out, on account of his thick skin and shell.