Like someone else mentioned here, they do not have to make the Shredder SUPERSHREDDER or anything.
There are several questions regarding this "universe's" Shredder? Did he really died? Where is his body? Did he died the same way like in the first movie?
The new movie didn't really answer these, so it's safe to say that they can "reinterpret" on how the Turtles supposedly "killed" The Shredder, and yet somehow he survived and not really dead as the Turtles would like to think. I did remember one scene when Leo said "Shredder is dead, who are you working for?" to Karai before Karai left, not answering anything. It could possibly be that Shredder a.k.a. Oruku Saki (the real man) is still running the organization.
Heck, the Uncle Ben's death scene was "reinterpreted" like I lost count how many in the sequels of SPIDER-MAN, so I'm sure it's not such a daunting task to "reinterpret" scenes that really didn't happen yet (i.e. the supposedly "death" and return of The Shredder).
Oh yeah, and please, no "mystic-worm-clone" stuff, and leave it to the comics, and please no "utrom-in-the-exosuit" Shredder (really hated those in the new Toon, he's basically Shredder and Krang combined in one character, and yet they HATED every characters from the old Toon).